MatSAM: a Matlab implementation for Significance Analysis of Microarrays

Microarray experiments enable the simultaneous measure of expression levels of large amount of genes and have many applications. A widespread one is finding set of genes that are differentially expressed. Significance Analysis of Microarrays (SAM) helps to produce those sets using multiple testing techniques. There is unfortunately not yet a public tool enabling to do SAM using the Matlab platform. We here define MatSAM, a SAM implementation in Matlab, and show that it yields results of high confidence comparatively to those obtained by putative tools available in the R programming environment. MatSAM can be used in conjunction with Matlab Bioinformatics toolbox to perform further analysis.Availability: MatSAM is available as source code at  http://www.bioinfoindia.org/MatSA

Activités Antiproliférative et Antiradicalaire d’extraits Aqueux de Quatre Plantes Médicinales Congolaises

Le but de ce travail est d’évaluer les propriétés antiproliférative et antiradicalaire des extraits aqueux de quatre plantes médicinales congolaises dont Morinda lucida, Klainedoxa gabonensis, Tephrosia vogelii et Nauclea latifolia. L’activité antiproliférative de l’extrait aqueux de chacune des quatre espèces a été évaluée in vitro sur une lignée cellulaire cancéreuse (U87-MG) et une lignée cellulaire normale (Hek-293) en utilisant le test MTT. L’activité antiradicalaire a été évaluée en mesurant la capacité de piégeage du radical DPPH. Des analyses phytochimiques des extraits ont été réalisées par chromatographie sur couche mince et par HPLC-PDA. Les extraits aqueux de Klainedoxa gabonenis et de Tephrosia vogelii ont montré une activité antiproliférative contre les cellules cancéreuses U87-MG avec des valeurs de CI50 inférieures à 90 μg/ml. L’extrait aqueux de Klainedoxa gabonenis a montré également une activité antiradicalaire remarquable (CI50 = 4 ± 0,73 μg/ml) .En plus, le traitement des cellules cancéreuses U87-MG à la fois par l’extrait aqueux de Klainedoxa gabonensis (100 μg/ml) et par un inhibiteur de la protéine MEK (1μM) provoque une suppression totale de la prolifération des cellules U87-MG (glioblastome). L’analyse en HPLC–PDA de l’extrait aqueux Klainedoxa gabonenis a montré la présence des composés de type acide gallique (41, 9 %) et quercétine (2,17 %). Notre étude a permis d’identifier deux plantes médicinales aux propriétés antiprolifératives parmi les quatre plantes médicinales congolaises évaluées dont une possédant à la fois les propriétés antiproliférative et antiradicalaire. The purpose of this work is to evaluate antiprolifertive and DPPH radical scavenging activities of aqueous extracts from Morinda lucida Smith, Klainedoxa gabonensis Pierre ex Engl, Tephrosia vogelii Hook f and Nauclea latifolia Sm. The antiproliferative activity of the aqueous extract of each of the four species was evaluated in vitro on a cancer cell line (U87-MG) and a normal cell line (Hek-293) using the MTT assay. The antiradicalar activity was evaluated by measuring the scavenger capacity of the DPPH radical. Phytochemical analyzes of the extract were performed by thin layer chromatography and HPLC-PDA. The aqueous extracts of Klainedoxa gabonenis and Tephrosia vogelii showed antiproliferative activity against U87-MG cancer cells with IC50 values below 90 μg / ml. The aqueous extract of Klainedoxa gabonenis also showed remarkable antiradical activity (IC50 = 4± 0,73 μg/ml). In addition, the treatment of U87-MG cancer cells by both the aqueous extract of Klainedoxa gabonensis (100 μg / ml) and by an MEK protein inhibitor (1 μM) causes a total suppression of U87-cell proliferation. MG (glioblastoma). HPLC-PDA analysis of the aqueous extract Klainedoxa gabonenis showed the presence of gallic acid compounds (41.9%) and Quercetin (2.17%).: Our study identified two medicinal plants with antiproliferative properties among the four Congolese herbal medicines evaluated, one with both anti-proliferative and antiradical properties

La sous-unité régulatrice de la phosphodiestérase photo-activable (interaction avec des protéines à domaine SH3 et localisation synaptique dans les photorécepteurs)

Dans les photorécepteurs, la phosphodiestérase 6 (PDE6) est régulée par le transfert de sa sous-unité régulatrice (P ). Des études récentes indiquent que P peut interagir avec des domaines SH3. Nous avons donc recherché les protéines contenant des domaines SH3 capables d'interagir avec P dans les photorécepteurs de rat. Une étude en double-hybride et GST " Pull-Down " nous a permis d'identifier cinq partenaires potentiels de P : deux protéines impliquées dans l'endocytose (l'amphiphysine et la PACSINE) et trois protéines impliquées dans la signalisation des récepteurs tyrosine kinases (Src, Grb2 et la P85-PI3K). Trois de ces protéines (l'amphiphysine, la PACSINE et la P85-PI3K) sont clairement exprimées dans les photorécepteurs. Cependant, seule la PACSINE s'est montrée capable d'interagir in vivo avec P au niveau des segments internes et des pédicules synaptiques des photorécepteurs, cette localisation est régulée par la lumière. Une étude portant sur le développement de la rétine de rat, nous a permis de détecter une expression de P dans les pédicules basaux des photorécepteurs sur des rats nouveaux nés (P0 à P5). Pour rechercher les possibles rôles de P dans la mise en place des synapses et la différenciation du photorécepteur, nous avons examiné les rétines de souris P rod -/-. Les observations en microscopie électronique révèlent une diminution de triades de bâtonnets correctement formées dans la plexiforme externe des souris P rod -/-. L'ensemble de ces résultats suggèrent que l'interaction P -PACSINE peut être impliquée dans l'endocytose au niveau des rubans synaptiques et que P est nécessaire à la différenciation des synapses des bâtonnet.In photoreceptors, phosphodiesterase 6 (PDE6) is regulated, due to the shuttling of its regulatory subunit (P ). Recent studies have indicated that P can interact with SH3 domains and that it can alter MAPK signalling. Therefore, we sought to identify SH3-containing proteins that might interact with P in rat photoreceptors.A yeast two-hybrid and GST Pull-Down assay allowed us to identify two proteins involved in endocytosis (amphiphysin and PACSIN) and three proteins involved in receptor tyrosine kinase signalling (Src, GRB2 and P85-PI3K), as putative partners of P .Three of these proteins (amphiphysin, PACSIN and P85-PI3K) were clearly expressed in photoreceptors. However, only PACSIN was found to interact in vivo with P in inner segments and synaptic pedicles of photoreceptors and that P concentration in synaptic pedicles increases in response to light.A developmental study allowed us to detect P expression in the retina of newborn rats (P0). At the early stages of retinogenesis (P0 to P5), P immunodetection was confined to basal pedicles of photoreceptors. A result suggesting that P might play a role in the establishment of photoreceptor synapses.To investigate the possible roles of P in photoreceptor differentiation, retinas of P rod -/- mice were examined. Electron microscopic observations revealed a deficit of well-defined rod triads in the outer plexiform layer of P rod -/- mice. Together, the data suggest that P -pacsin interaction may contribute to specific characteristics of the endocytic mechanism at the ribbon synapse of photoreceptors and that P is required for optimal differentiation of rod synapses.POITIERS-BU Sciences (861942102) / SudocSudocFranceF

Is-ClusterMPP: clustering algorithm through point processes and influence space towards high-dimensional data

International audienceClustering via Marked Point Processes and Influence Space, Is-ClusterMPP, is a new unsupervised clustering algorithm through adaptive MCMC sampling of a Marked point processes of interacting balls. The chosen Gibbs energy cost function makes use of k-influence space information. It detects clusters of different shapes, sizes and unbalanced local densities. It aims at dealing also with high-dimensionaland scalable datasets. Is-ClusterMPP solves the problem of local heterogeneity in densities and prevents the impact of the global density in the detection of unbalanced classes, by using the k-influence space. This concept reduces also the input values amount. The curse of dimensionality is handled by using a local subspace clustering principal embedded in a weighted similarity metric. Balls are constituting aconfiguration sampled from the Marked point process. Due to the choice of the energy, they tends to cover neighboring data, then considered sharing the same cluster set. The energy is balancing different goals. (1) The data driven objective function is provided according to k-influence space. Data in a high-dense region are favored to be covered by a ball. (2) An interaction part in the energy prevents theballs full overlap phenomenon and favors connected groups of balls. The algorithm, Markov dynamics, does converge towards configurations sampled from the MPP model. This algorithm has been applied in real benchmarks through gene expression data of various sizes. Different experiments have been done to compare Is-ClusterMPP against the most well-known clustering algorithms and its efficiency is claimed

Anti-Human FSH Receptor Monoclonal Antibodies: Immunochemical and Immunocytochemical Characterization of the Receptor

International audienceThe extracellular domain of the human FSH receptor was expressed in Escherichia coli as a fusion protein with ubiquitin. It was tagged with a poly-His tract which was used for its purification. Immunization of mice allowed the preparation of high affinity antireceptor monoclonal antibodies. The latter fell into two categories:  some of them were inhibited hormone binding and adenylate cyclase activation whereas others were devoid of these properties. None of the antibodies had agonistic activity (i.e., stimulated adenylate cyclase). Immunoaffinity chromatography allowed us to purify the native receptor in a single step either from a permanently transfected L cell line (75% recovery) or from human ovaries (33% recovery). Immunoblotting of the receptor in human ovaries showed the presence of a major band of 87 kDa and of a minor band of 81 kDa. Endoglycosidase digestion and pulse−chase experiments showed the former to be the mature receptor and the latter the precursor containing mannose-rich carbohydrates. Thus, as in the case for the LH receptor, there was an accumulation (albeit to a lower degree) of the precursor in target cells. We did not detect variant forms of the protein corresponding to the alternative mRNA transcripts previously described. Additive binding to the receptor of several antibodies, but not of the same antibody, allowed us to establish a sandwich-type ELISA for the receptor (sensitivity ∼1 fmol) and to obtain evidence against the existence of previously described oligomeric forms of the protein. All monoclonal antibodies were able to label the receptor immunocytochemically in transfected cells, and two of them were also able to detect it at the markedly lower physiological concentrations, i.e., in human Sertoli and granulosa cells

Exceptional preservation of eye structure in arthropod visual predators from the Middle Jurassic

Vision has revolutionized the way animals explore their environment and interact with each other and rapidly became a major driving force in animal evolution. However, direct evidence of how ancient animals could perceive their environment is extremely difficult to obtain because internal eye structures are almost never fossilized. Here, we reconstruct with unprecedented resolution the three-dimensional structure of the huge compound eye of a 160-million-year-old thylacocephalan arthropod from the La Voulte exceptional fossil biota in SE France. This arthropod had about 18,000 lenses on each eye, which is a record among extinct and extant arthropods and is surpassed only by modern dragonflies. Combined information about its eyes, internal organs and gut contents obtained by X-ray microtomography lead to the conclusion that this thylacocephalan arthropod was a visual hunter probably adapted to illuminated environments, thus contradicting the hypothesis that La Voulte was a deep-water environment

ClusterMPP: An unsupervised density-based clustering algorithm via Marked Point Process

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A microbiota-root-shoot circuit favours Arabidopsis growth over defence under suboptimal light

A synthetic root microbial community rescues weak growth under low light and enhances immunity in Arabidopsis. Transcription factor MYC2 regulates both this coordination between rhizosphere and shoots and the growth/defence trade-off under low light conditions. Bidirectional root-shoot signalling is probably key in orchestrating stress responses and ensuring plant survival. Here, we show that Arabidopsis thaliana responses to microbial root commensals and light are interconnected along a microbiota-root-shoot axis. Microbiota and light manipulation experiments in a gnotobiotic plant system reveal that low photosynthetically active radiation perceived by leaves induces long-distance modulation of root bacterial communities but not fungal or oomycete communities. Reciprocally, microbial commensals alleviate plant growth deficiency under low photosynthetically active radiation. This growth rescue was associated with reduced microbiota-induced aboveground defence responses and altered resistance to foliar pathogens compared with the control light condition. Inspection of a set of A. thaliana mutants reveals that this microbiota- and light-dependent growth-defence trade-off is directly explained by belowground bacterial community composition and requires the host transcriptional regulator MYC2. Our work indicates that aboveground stress responses in plants can be modulated by signals from microbial root commensals

Detection of dicentric chromosome (9;20) in paediatric B-cell acute lymphoblastic leukaemia: prognostic significance

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