Prédiction de gènes parallélisée de haute performance dans MATLAB

Ce travail s’inscrit dans un cadre de recherche global du génome humain. Il s'intéresse particulièrement à l'identification de milliers de gènes qui demeurent toujours inconnus à ce jour. Afin de pouvoir effectuer cette tâche sur une plateforme informatique, les séquences d’acide désoxyribonucléique (ADN) seront traitées comme étant des signaux pour permettre l’usage des techniques en traitement numérique de signaux (TNS). Cette approche permettra de réduire les coûts et surtout, le temps que prennent les chercheurs à trouver un gène impliqué dans une maladie. Le projet est divisé en deux volets. Le premier volet de cette recherche consiste à réduire de façon importante les temps de calcul de certains algorithmes en bio-informatique. Cette recherche propose une méthode de mise en oeuvre des algorithmes de prédiction de gènes en parallèle avec le logiciel MATLAB. Les approches proposées sont basées soit sur l’algorithme de Goertzel ou de FFT en utilisant diverses procédures de parallélisme sur une unité centrale de traitement (CPU) et à une unité de processeur graphique (GPU). Les résultats montrent que l’utilisation d’une approche simple, c’est-à-dire sans modification de l’implémentation dans MATLAB, peut nécessiter plus de 4 h et demie pour le traitement de 15 millions de paires de bases (pb) alors qu’une implémentation optimisée peut effectuer la même tâche en moins d’une minute. Nous avons obtenu les meilleurs résultats avec l’implémentation sur GPU qui a pu compléter l'analyse en 57 s, ce qui est plus de 270 fois plus rapide qu’une approche conventionnelle. Ce premier volet de recherche propose deux stratégies pour accélérer le traitement des données du génome humain et s’appuie sur les différents mécanismes de parallélisation. Lorsque l'implantation se fait avec un CPU, les résultats indiquent qu'il serait préférable d'utiliser une fonction de bas niveau (MEX) afin d'augmenter la vitesse d’exécution. De plus, l'usage des boucles parallèles (PARFOR) doit être effectué dans un ordre précis pour bénéficier au maximum du parallélisme dans l’implantation de Goertzel. Lorsque l'implantation est exécutée sur le GPU, les données doivent être segmentées en plus petits blocs afin d'optimiser les temps de traitement. En effet, les blocs qui sont trop gros risquaient de dépasser la taille de la mémoire tandis que des blocs trop petits ne permettaient pas à l'usager de bénéficier pleinement du parallélisme. Dans le second volet, nous avons poursuivi avec l’implantation d’un second algorithme qui permet de cibler les régions susceptibles à la présence de gènes. Cet algorithme se base sur les hexamères qui sont de courtes séquences d’ADN composées de 6 nucléotides. De toutes les variations d’hexamères possibles (4096), seulement 40 de celles-ci se retrouvent plus souvent dans les régions codantes que non codantes. Les autres hexamères se retrouvent autant dans les introns que dans les exons. Il est donc possible de survoler les séquences d’ADN et, selon la présence ou l’absence de certains hexamères, de prédire quelles régions sont codantes. Lors de la superposition des deux approches, soit l’analyse en fréquence et l’analyse des hexamères, il est possible de mieux cibler les zones où l’on peut retrouver de nouveaux gènes. Les analyses effectuées avec les différents algorithmes présentent des valeurs qui témoignent de la probabilité de retrouver un gène dans une région donnée. Pour compléter le processus de prédiction, il est important de déterminer un critère à partir duquel le programme décide qu’il s’agit réellement d’un gène. Ce critère est basé sur trois paramètres, soient le seuil positif, le seuil négatif et taille de la fenêtre. Afin de déterminer les valeurs optimales, les trois paramètres ont été balayés et la meilleure combinaison a été identifiée. L’approche proposée dans ce mémoire permet d’analyser de grandes séquences d’ADN en peu de temps afin d’identifier des zones susceptibles de coder un gène. Ce processus est important puisqu’on estime qu’il reste encore quelques milliers de gènes inconnus qui peuvent être responsables de plusieurs maladies génétiques. Nous espérons que ce travail contribuera à la découverte de nouveaux gènes pour ainsi mieux diagnostiquer certaines maladies génétiques

The MEK2-binding tumor suppressor hDlg is recruited by E-cadherin to the midbody ring

Background: The human homologue of the Drosophila Discs-large tumor suppressor protein, hDlg, is a multi-domain cytoplasmic protein that localizes to the membrane at intercellular junction sites. At both synaptic junctions and epithelia cell-cell junctions, hDlg is known to recruit several signaling proteins into macromolecular complexes. hDlg is also found at the midbody, a small microtubule-rich structure bridging the two daughter cells during cytokinesis, but its function at this site is not clear. Results: Here we describe the interaction of hDlg with the activated form of MEK2 of the canonical RAF/MEK/ERK pathway, a protein that is found at the midbody during cytokinesis. We show that both proteins localize to a sub-structure of the midbody, the midbody ring, and that the interaction between the PDZ domains of hDlg and the C-terminal portion of MEK2 is dependent on the phosphorylation of MEK2. Finally, we found that E-cadherin also localizes to the midbody and that its expression is required for the isoform-specific recruitment of hDlg, but not activated MEK2, to that structure. Conclusion: Our results suggest that like at other cell-cell junction sites, hDlg is part of a macromolecular complex of structural and signaling proteins at the midbody.Molecular and Cellular Biolog

Representation of Objects in Space by Two Classes of Hippocampal Pyramidal Cells

Humans can recognize and navigate in a room when its contents have been rearranged. Rats also adapt rapidly to movements of objects in a familiar environment. We therefore set out to investigate the neural machinery that underlies this capacity by further investigating the place cell–based map of the surroundings found in the rat hippocampus. We recorded from single CA1 pyramidal cells as rats foraged for food in a cylindrical arena (the room) containing a tall barrier (the furniture). Our main finding is a new class of cells that signal proximity to the barrier. If the barrier is fixed in position, these cells appear to be ordinary place cells. When, however, the barrier is moved, their activity moves equally and thereby conveys information about the barrier's position relative to the arena. When the barrier is removed, such cells stop firing, further suggesting they represent the barrier. Finally, if the barrier is put into a different arena where place cell activity is changed beyond recognition (“remapping”), these cells continue to discharge at the barrier. We also saw, in addition to barrier cells and place cells, a small number of cells whose activity seemed to require the barrier to be in a specific place in the environment. We conclude that barrier cells represent the location of the barrier in an environment-specific, place cell framework. The combined place + barrier cell activity thus mimics the current arrangement of the environment in an unexpectedly realistic fashion

The interaction of lean and building information modeling in construction

Lean construction and Building Information Modeling are quite different initiatives, but both are having profound impacts on the construction industry. A rigorous analysis of the myriad specific interactions between them indicates that a synergy exists which, if properly understood in theoretical terms, can be exploited to improve construction processes beyond the degree to which it might be improved by application of either of these paradigms independently. Using a matrix that juxtaposes BIM functionalities with prescriptive lean construction principles, fifty-six interactions have been identified, all but four of which represent constructive interaction. Although evidence for the majority of these has been found, the matrix is not considered complete, but rather a framework for research to explore the degree of validity of the interactions. Construction executives, managers, designers and developers of IT systems for construction can also benefit from the framework as an aid to recognizing the potential synergies when planning their lean and BIM adoption strategies

Bostonia

Founded in 1900, Bostonia magazine is Boston University's main alumni publication, which covers alumni and student life, as well as university activities, events, and programs

Synthetic anionic surfaces can replace microparticles in stimulating burst coagulation of blood plasma

Biomaterials are frequently evaluated for pro-coagulant activity but usually in the presence of microparticles (MPs), cell-derived vesicles in blood plasma whose phospholipid surfaces allow coagulation factors to set up as functional assemblies. We tested the hypothesis that synthetic anionic surfaces can catalyze burst thrombin activation in human blood plasma in the absence of MPs. In a thromboelastography (TEG) assay with plastic sample cups and pins, recalcified human citrated platelet-poor plasma spontaneously burst-coagulated but with an unpredictable clotting time whereas plasma depleted of MPs by ultracentrifugation failed to coagulate. Coagulation of MP-depleted plasma was restored in a dose-dependent manner by glass microbeads, hydroxyapatite nanoparticles (HA NPs), and carboxylic acid-containing anionic nanocoatings of TEG cups and pins (coated by glow-discharge plasma-polymerized ethylene containing oxygen, L-PPE:O with 4.4 and 6.8 atomic % [COOH]). Glass beads lost their pro-coagulant activity in MP-depleted plasma after their surfaces were nanocoated with hydrophobic plasma-polymerized hexamethyl disiloxane (PP-HMDSO). In FXII-depleted MP-depleted plasma, glass microbeads failed to induce coagulation, however, FXIa was sufficient to induce coagulation in a dose-dependent manner, with no effect of glass beads. These data suggest that anionic surfaces of crystalline, organic, and amorphous solid synthetic materials catalyze explosive thrombin generation in MP-depleted plasma by activating the FXII-dependent intrinsic contact pathway. The data also show that microparticles are pro-coagulant surfaces whose activity has been largely overlooked in many coagulation studies to-date. These results suggest a possible mechanism by which anionic biomaterial surfaces induce bone healing by contact osteogenesis, through fibrin clot formation in the absence of platelet activation.Fil: Contreras García, Angel. École Polytechnique de Montréal. Department of Engineering Physics. Groupe de Physique et Technologie des Couches Minces; CanadáFil: D'elía, Noelia Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Química del Sur. Universidad Nacional del Sur. Departamento de Química. Instituto de Química del Sur; Argentina. École Polytechnique de Montréal. Department of Engineering Physics; CanadáFil: Desgagné, Maxime. École Polytechnique de Montréal. Department of Engineering Physics; CanadáFil: Lafantaisie Favreau, Charles Hubert. École Polytechnique de Montréal. Department of Engineering Physics; CanadáFil: Rivard, Georges Étienne. CHU Sainte-Justine; CanadáFil: Ruiz, Juan Carlos. Universidad Autónoma Metropolitana; MéxicoFil: Wertheimer, Michael Robert. École Polytechnique de Montréal. Department of Engineering Physics. Groupe de Physique et Technologie des Couches Minces; Canadá. École Polytechnique de Montréal. Institute of Biomedical Engineering; CanadáFil: Messina, Paula Verónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Química del Sur. Universidad Nacional del Sur. Departamento de Química. Instituto de Química del Sur; ArgentinaFil: Hoemann, Caroline Dieckmann. École Polytechnique de Montréal. Department of Engineering Physics; Canadá. École Polytechnique de Montréal. Institute of Biomedical Engineering; Canad

Kloning Manusia

In the last few years, very rapid progress in the cloning technology and its development towards human cloning has become a hotly-debated issue. Cloning, which is the process of formation of a number of individuals with the same genetic structure, can be done by means of embryo-splitting method and nuclear transfer. Human cloning through the nuclear transfer method is directed towards two purposes, i.e. reproduction and therapy. The relatively new transgenic technology can be combined with the cloning technique to produce clones with new genes. However, pros and cons arise concerning the development of research on human cloning, particularly cloning for reproductive purposes. Therefore, there is need for a moratorium period before human cloning can be performed in order that solutions for all kinds of problems related to safety and ethics can be found

NHC‐Stabilized Mixed Group 13/14/15 Element Hydrides

The syntheses of novel N-heterocyclic carbene (NHC) adducts of group 13, 14 and 15 element hydrides are reported. Salt metathesis reactions between NaPH2 and IDipp ⋅ GeH2BH2OTf (1) (IDipp=1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) led to mixtures of the two isomers IDipp ⋅ GeH2BH2PH2 (2 a) and IDipp ⋅ BH2GeH2PH2 (2 b); by altering the reaction conditions an almost exclusive formation of 2 b was achieved. Attempts to purify mixtures of 2 a and 2 b by re-crystallization from THF afforded a salt [IDipp ⋅ GeH2BH2 ⋅ IDipp][PHGeH2BH2PH2BH2GeH2] (4) that contains the novel anionic cyclohexyl-like inorganic heterocycle [PHGeH2BH2PH2BH2GeH2]−. In addition, the borane adducts IDipp ⋅ GeH2BH2PH2BH3 (3 a) and IDipp ⋅ BH2GeH2PH2BH3 (3 b) as even longer chain compounds were obtained from reactions of 2 a/2 b with H3B ⋅ SMe2 and were studied by NMR spectroscopy. Accompanying DFT computations give insight into the mechanism and energetics associated with 2 a/2 b isomerization as well as their decomposition pathways

Le FORUM, Vol. 35 No. 2

https://digitalcommons.library.umaine.edu/francoamericain_forum/1030/thumbnail.jp

Land-based measures to mitigate climate change : potential and feasibility by country

Acknowledgements The design of this study and the data generated was guided by expert consultations and relied on the help of many. We thank all those who contributed: Sierra Gladfelter, Jo House, Mercedes Bustamante, Susan Cook-Patton, Sara Leavitt, Nick Wolff, and Thomas Worthington. We thank M.-J. Valentino at Imaginary Office for helping to design the first three figures. This work was supported by the authors’ institutions and funding sources, including the Climate and Land-use Alliance, the Dutch Ministry of Agriculture, Nature Management and Food Quality, and the EU H2020 projects VERIFY and ENGAGE (grant agreement no. 821471).Peer reviewedPublisher PD