Classification non supervisée par HMM de sites de fixation de facteurs de transcription chez les bactéries

Colloque avec actes et comité de lecture. nationale.National audienceNous développons des méthodes de fouille de données basées sur l'utilisation de modèles Markoviens du second ordre adaptés à l'étude des génomes. Ceux-ci réalisent une segmentation pouvant être observée sous la forme d'un signal stochastique traduisant l'organisation et la structure des motifs d'ADN sous-jacents. Aucune hypothèse 'a priori' n'est effectuée sur le contenu génétique des séquences étudiées. La modélisation du corpus de séquences est réalisée par une étape d'apprentissage automatique qui produit une classification non supervisée des segments nucléotidiques observés sur les différents états des HMM. Une première étape d'apprentissage sur les séquences chromosomiques complètes des bactéries actinomycètes Streptomyces coelicolor, S. avermitilis et Mycobacterium tuberculosis permet l'obtention de trois classes de HMM décrivant chacune un génome. Lors du processus de segmentation, certaines chaînes d'états cachés décrivent des fragments génomiques comme les gènes et les séquences intergéniques alors qu'une autre chaîne se spécialise sur la distribution de motifs d'ADN locaux particuliers. Ceux-ci correspondent à des mots de 5 à 12 nucléotides présents à des fréquences inhabituelles dans les régions intergéniques. Chez S. coelicolor, la classification de 2500 de ces motifs, issus d'une extraction automatique et identifiés dans 1,2 Mb d'ADN génomique, indique que 7% correspondraient à des sites de fixation de facteurs sigma connus (SigR, SigB, WhiG, HrdB) et 5% à des sites de fixation du ribosome ou des terminateurs de transcription potentiels. Concernant le régulon SigR/SigH (réponse au stress oxydant chez les Streptomyces/M. tuberculosis), la mise en oeuvre de cette approche a permis de détecter tous les promoteurs déjà déterminés biologiquement. Enfin, certains de ces motifs ne peuvent être corrélés à des rôles biologiques connus ou prédits à ce jour. Leur classification pourrait mettre en évidence des groupes à propriétés communes et viserait à définir des motifs promoteurs, puis, à terme, des réseaux de gènes co-régulés

Design and Synthesis of Thiazolo[5,4-f]quinazolines as DYRK1A Inhibitors, Part I

International audienc

Multiple and Variable NHEJ-Like Genes Are Involved in Resistance to DNA Damage in Streptomyces ambofaciens

International audienceNon-homologous end-joining (NHEJ) is a double strand break (DSB) repair pathway which does not require any homologous template and can ligate two DNA ends together. The basic bacterial NHEJ machinery involves two partners: the Ku protein, a DNA end binding protein for DSB recognition and the multifunctional LigD protein composed a ligase, a nuclease and a polymerase domain, for end processing and ligation of the broken ends. In silico analyses performed in the 38 sequenced genomes of Streptomyces species revealed the existence of a large panel of NHEJ-like genes. Indeed, ku genes or ligD domain homologues are scattered throughout the genome in multiple copies and can be distinguished in two categories: the " core " NHEJ gene set constituted of conserved loci and the " variable " NHEJ gene set constituted of NHEJ-like genes present in only a part of the species. In Streptomyces ambofaciens ATCC23877, not only the deletion of " core " genes but also that of " variable " genes led to an increased sensitivity to DNA damage induced by electron beam irradiation. Multiple mutants of ku, ligase or polymerase encoding genes showed an aggravated phenotype compared to single mutants. Biochemical assays revealed the ability of Ku-like proteins to protect and to stimulate ligation of DNA ends. RT-qPCR and GFP fusion experiments suggested that ku-like genes show a growth phase dependent expression profile consistent with their involvement in DNA repair during spores formation and/or germination

A new exactly solvable quantum model in N dimensions

An N-dimensional position-dependent mass Hamiltonian (depending on a parameter \lambda) formed by a curved kinetic term and an intrinsic oscillator potential is considered. It is shown that such a Hamiltonian is exactly solvable for any real positive value of the parameter \lambda. Algebraically, this Hamiltonian can be thought of as a new maximally superintegrable \lambda-deformation of the N-dimensional isotropic oscillator and, from a geometric viewpoint, this system is just the intrinsic oscillator potential on an N-dimensional hyperbolic space with nonconstant curvature. The spectrum of this model is shown to be hydrogenlike, and their eigenvalues and eigenfunctions are explicitly obtained by deforming appropriately the symmetry properties of the N-dimensional harmonic oscillator. A further generalization of this construction giving rise to new exactly solvable models is envisaged.Comment: 12 pages, 2 figures; comments added and typos correcte

Specificity and Mechanism of Action of EHT 1864, a Novel Small Molecule Inhibitor of Rac Family Small GTPases

There is now considerable experimental evidence that aberrant activation of Rho family small GTPases promotes the uncontrolled proliferation, invasion, and metastatic properties of human cancer cells. Therefore, there is considerable interest in the development of small molecule inhibitors of Rho GTPase function. However, to date, most efforts have focused on inhibitors that indirectly block Rho GTPase function, by targeting either enzymes involved in post-translational processing or downstream protein kinase effectors. We recently determined that the EHT 1864 small molecule can inhibit Rac function in vivo. In this study, we evaluated the biological and biochemical specificities and biochemical mechanism of action of EHT 1864. We determined that EHT 1864 specifically inhibited Rac1-dependent platelet-derived growth factor-induced lamellipodia formation. Furthermore, our biochemical analyses with recombinant Rac proteins found that EHT 1864 possesses high affinity binding to Rac1, as well as the related Rac1b, Rac2, and Rac3 isoforms, and this association promoted the loss of bound nucleotide, inhibiting both guanine nucleotide association and Tiam1 Rac guanine nucleotide exchange factor-stimulated exchange factor activity in vitro. EHT 1864 therefore places Rac in an inert and inactive state, preventing its engagement with downstream effectors. Finally, we evaluated the ability of EHT 1864 to block Rac-dependent growth transformation, and we determined that EHT 1864 potently blocked transformation caused by constitutively activated Rac1, as well as Rac-dependent transformation caused by Tiam1 or Ras. Taken together, our results suggest that EHT 1864 selectively inhibits Rac downstream signaling and transformation by a novel mechanism involving guanine nucleotide displacement

A new data mining approach for the detection of bacterial promoters combining stochastic and combinatorial methods

International audienceWe present a new data mining method based on stochastic analysis (HMM for Hidden Markov Model) and combinatorial methods for discovering new transcriptional factors in bacterial genome sequences. Sigma factor binding sites (SFBSs) were described as patterns of box1 - spacer - box2 corresponding to the -35 and -10 DNA motifs of bacterial promoters. We used a high-order Hidden Markov Model in which the hidden process is a second-order Markov chain. Applied on the genome of the model bacterium Streptomyces coelicolor (2), the a posteriori state probabilities revealed local maxima or peaks whose distribution was enriched in the intergenic sequences (``iPeaks'' for intergenic peaks). Short DNA sequences underlying the iPeaks were extracted and clustered by a hierarchical classification algorithm based on the SmithWaterman local similarity. Some selected motif consensuses were used as box1 (-35 motif) in the search of a potential neighbouring box2 (-10 motif) using a word enumeration algorithm. This new SFBS mining methodology applied on Streptomyces coelicolor was successful to retrieve already known SFBSs and to suggest new potential transcriptional factor binding sites (TFBSs). The well defined SigR regulon (oxidative stress response) was also used as a test quorum to compare first and second-order HMM. Our approach also allowed the preliminary detection of known SFBSs in Bacillus subtilis

Phosphorylation of CLEC-2 is dependent on lipid rafts, actin polymerization,secondary mediators, and Rac

The C-type lectin-like receptor 2 (CLEC-2)activates platelets through Src and Syk tyrosine kinases via a single cytoplasmic YxxL motif known as a hem immunoreceptor tyrosine-based activation motif (hemITAM).Here, we demonstrate using sucrose gradient ultracentrifugation and methyl--cyclodextrin treatment that CLEC-2 translocates to lipid rafts upon ligand engagement and that translocation is essential for hemITAM phosphorylation and signal initiation. HemITAM phosphorylation, but not translocation, is also critically dependent on actin polymerization,Rac1 activation, and release of ADP and thromboxane A2 (TxA2). The role of ADP and TxA2 in mediating hosphorylation is dependent on ligand engagement and rac activation but is independent of platelet aggregation. In contrast,tyrosine phosphorylation of the GPVIFcR -chain ITAM, which has 2 YxxL motifs,is independent of actin polymerization and secondary mediators. These results reveal a unique series of proximal events in CLEC-2 phosphorylation involving actin polymerization, secondary mediators,and Rac activation

Quantum mechanics on spaces of nonconstant curvature: the oscillator problem and superintegrability

The full spectrum and eigenfunctions of the quantum version of a nonlinear oscillator defined on an N-dimensional space with nonconstant curvature are rigorously found. Since the underlying curved space generates a position-dependent kinetic energy, three different quantization prescriptions are worked out by imposing that the maximal superintegrability of the system has to be preserved after quantization. The relationships among these three Schroedinger problems are described in detail through appropriate similarity transformations. These three approaches are used to illustrate different features of the quantization problem on N-dimensional curved spaces or, alternatively, of position-dependent mass quantum Hamiltonians. This quantum oscillator is, to the best of our knowledge, the first example of a maximally superintegrable quantum system on an N-dimensional space with nonconstant curvature.Comment: 26 pages, 5 figure

On two superintegrable nonlinear oscillators in N dimensions

We consider the classical superintegrable Hamiltonian system given by $H=T+U={p^2}/{2(1+\lambda q^2)}+{{\omega}^2 q^2}/{2(1+\lambda q^2)}$, where U is known to be the "intrinsic" oscillator potential on the Darboux spaces of nonconstant curvature determined by the kinetic energy term T and parametrized by {\lambda}. We show that H is Stackel equivalent to the free Euclidean motion, a fact that directly provides a curved Fradkin tensor of constants of motion for H. Furthermore, we analyze in terms of {\lambda} the three different underlying manifolds whose geodesic motion is provided by T. As a consequence, we find that H comprises three different nonlinear physical models that, by constructing their radial effective potentials, are shown to be two different nonlinear oscillators and an infinite barrier potential. The quantization of these two oscillators and its connection with spherical confinement models is briefly discussed.Comment: 11 pages; based on the contribution to the Manolo Gadella Fest-60 years-in-pucelandia, "Recent advances in time-asymmetric quantum mechanics, quantization and related topics" hold in Valladolid (Spain), 14-16th july 201