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1. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

Giancarlo Perrone, Anna Lipzen, Igor V. Grigoriev, Ana Ramón, Claudio Scazzocchio, Karin M. Overkamp, David Cánovas, Alan Kuo, George Diallinas, Kristiina Hildén, Tabea Schütze, Asaf Salamov, Patricia A. vanKuyk, Anthony Levasseur, Cindy Choi, Tamás Emri, Bernard Henrissat, Erzsébet Sándor, Gerhard H. Braus, Evy Battaglia, Camila Caldana, María Harispe, Kurt LaButti, Nadhira Salih, Andrew MacCabe, Renato Augusto Corrêa dos Santos, Stefan Rauscher, Guillermo Aguilar-Osorio, François Piumi, Ellen Lagendijk, Axel A. Brakhage, Giuseppina Mulè, David B. Archer, Cristiane Uchima, André Damasio, Nada Kraševec, Tammi Camilla Vesth, Petter Melin, Rob Habgood, Susanna A. Braus-Stromeyer, Gavin Sherlock, Mojtaba Asadollahi, Marion Askin, Abeer Hossain, Miia R. Mäkelä, Fusheng Chen, Erzsébet Fekete, Natalia Mielnichuk, Márton Miskei, Jennifer R. Wortman, Diego Mauricio Riaño-Pachón, Manuel Sanguinetti, Ákos Molnár, Alicia Clum, Jaap Visser, Scott E. Baker, Jos Houbraken, Eric Record, Reinhard Fischer, Rob Samson, Isabelle Benoit, Christos Gournas, Kristina Sepčić, Harald Kusch, Paul S. Dyer, Diana van Rossen-Uffink, Nathalie van de Wiele, Antonio F. Logrieco, Eugenia Karabika, Jean Paul Ouedraogo, Roberto Ruller, Juliana Velasco de Castro Oliveira, Alla Lapidus, Gustavo C. Cerqueira, Margarita Orejas, Miaomiao Zhou, Vicky Sophianopoulou, Vera Meyer, Chew Yee Ngan, Levente Karaffa, Shiela E. Unkles, Hee-Soo Park, Iran Malavazi, Antonia Gallo, Sotiris Amillis, Adrian Tsang, Julian Röhrig, Ekaterina Shelest, Jens Christian Frisvad, Bernhard Seiboth, Tiziano Benocci, Ad Wiebenga, Erzsébet Orosz, Erika Lindquist, Gregor Anderluh, Vincent Robert, Ryan Hope, Matthieu Hainaut, Robert Riley, Ronald P. de Vries, Gustavo H. Goldman, Mikael Rørdam Andersen, István Pócsi, Zsolt Karányi, Hui Sun, Richard B. Todd, Jae-Hyuk Yu, Wanping Chen, Özgür Bayram, Berl R. Oakley, Antonia Susca, Michel Flipphi, Fabio M. Squina, Susanne Freyberg, Arthur F. J. Ram, Peter J. Punt, Kerrie Barry, US Department of Energy Joint Genome Institute, Walnut Creek CA, USA, Fungal Physiology, CBS‑KNAW Fungal Biodiversity Centre and Fungal, Utrecht University [Utrecht], Department for Molecular Biology and Nanobiotechnology, National Institute of chemitry, Slovenia, United States Department of Energy, Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Centre for Research in Neurodegenerative Diseases, University of Toronto, US Department of Energy Joint Genome Institute, U.S Department of Energy, U.S. Department of Energy [Washington] (DOE)-U.S. Department of Energy [Washington] (DOE), Faculty of Biology, University of Athens, Panepistimioupolis, University of Athens, Panepistimioupolis, Dept. of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Joint Genome Institute, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Department of Molecular Microbiology and Biotechnology, Leiden University, Institute of Biology Leiden, The Netherlands & Kluyver Centre for Genomics of Industrial Fermentation, Institute of Sciences of Food Production (ISPA), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Biologie du Développement et Reproduction (BDR), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Sección Bioquímica, Depto. de Biología Celular y Molecular, Facultad de Ciencias (UDELAR), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Biodiversité et Biotechnologie Fongiques (BBF), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), University of Potsdam = Universität Potsdam, Institut Polytechnique des Sciences Avancées (IPSA), Institut de Mécanique Céleste et de Calcul des Ephémérides (IMCCE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Department of Plant Protection, University of Debrecen Egyetem [Debrecen], Stanford University, Istituto Scienze delle Produzioni Alimentari (ISPA), Centre for Structural and Functional Genomics, Concordia University [Montreal], School of Life Sciences, University of Nottingham, UK (UON), Dept Syst Biol, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Departement of Microbiology, Imperial College London, Research division biotechnology and microbiology, Institute of chemical engineering, Technische Univeritt Wien, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], School of Biology, Hungarian Scientific Research Fund K100464 NN116519 TAMOP 4.2.1./B-09/1/KONV-2010-0007 SROP-4.2.2.B-15/1/KONV-2015-001 / MINECO/FEDER AGL2011-29925 AGL2015-66131-AGL2015-66131-C2-2-R, Department of Food and Nutrition, Fungal Genetics and Biotechnology, European Commission, Ministerio de Economía y Competitividad (España), Westerdijk Fungal Biodiversity Institute, Westerdijk Fungal Biodiversity Institute - Fungal Physiology, Westerdijk Fungal Biodiversity Institute - Software and Databasing, Westerdijk Fungal Biodiversity Institute - Food and Indoor Mycology, COMBE, Isabelle, Consiglio Nazionale delle Ricerche (CNR), Consiglio Nazionale delle Ricerche [Roma] (CNR), Molecular Microbiology & Genetics, Georg-August-University [Göttingen], U.S. Department of Energy (DOE)-U.S. Department of Energy (DOE), INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), University of Helsinki, Institut National de la Recherche Agronomique (INRA), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Universität Potsdam, PSL Research University (PSL)-PSL Research University (PSL)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), University of Debrecen, Stanford University [Stanford], Technical University of Denmark [Lyngby] (DTU), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Universidad de Sevilla. Departamento de Genética, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), U.S. Department of Energy ( DOE ) -U.S. Department of Energy ( DOE ), Architecture et fonction des macromolécules biologiques ( AFMB ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes ( URMITE ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -IFR48, INSB-INSB-Centre National de la Recherche Scientifique ( CNRS ), Institut Hospitalier Universitaire Méditerranée Infection ( IHU AMU ), DOE Joint Genome Institute, Institute of Sciences of Food Production ( ISPA ), National Research Council [Italy] ( CNR ), Biologie du Développement et Reproduction ( BDR ), Institut National de la Recherche Agronomique ( INRA ), Facultad de Ciencias ( UDELAR ), Polytech Marseille ( AMU POLYTECH ), Aix Marseille Université ( AMU ), Biodiversité et Biotechnologie Fongiques ( BBF ), Institut National de la Recherche Agronomique ( INRA ) -Aix Marseille Université ( AMU ) -Ecole Centrale de Marseille ( ECM ), Institut für Biochemie und Biologie, Institut Polytechnique des Sciences Avancées ( IPSA ), IPSA, Institut de Mécanique Céleste et de Calcul des Ephémérides ( IMCCE ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Observatoire de Paris-Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Istituto Scienze delle Produzioni Alimentari ( ISPA ), Consiglio Nazionale delle Ricerche [Roma] ( CNR ), Concordia University [Montreal, Canada], University of Nottingham, UK ( UON ), Technical University of Denmark [Lyngby] ( DTU ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Broad Institute of MIT and Harvard ( BROAD INSTITUTE ), and Broad Institute of MIT and Harvard

Subjects
0301 basic medicine, champignon, Adaptation, Biological, Secondary Metabolism, Biológiai tudományok, Genome, Fungal biology, Cytochrome P-450 Enzyme System, Természettudományok, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Gene Expression Regulation, Fungal, Gene Regulatory Networks, Biomass, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Phylogeny, Fungal protein, Phylogenetic tree, biology, Microbiology and Parasitology, 1184 Genetics, developmental biology, physiology, Biodiversity, Genomics, Plants, Microbiologie et Parasitologie, 3. Good health, [ SDV.MHEP.MI ] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Aspergillus, séquençage du génome, BBSRC, Multigene Family, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genome sequencing, Comparative genomics, Genome, Fungal, Oxidoreductases, Biologie, Aspergillis, Metabolic Networks and Pathways, Signal Transduction, Life sciences, 030106 microbiology, education, FILOGENIA, Fungal Proteins, 03 medical and health sciences, Phylogenetics, Stress, Physiological, ddc:570, Genetic model, Humans, biodiversité fongique, génomique comparative, Research, aspergillus, RCUK, Computational Biology, Molecular Sequence Annotation, 15. Life on land, DNA Methylation, biology.organism_classification, Carbon, Evolutionary biology, 1182 Biochemistry, cell and molecular biology
Abstract

[Background] The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus., [Results] We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli., [Conclusions] Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi., The sugar transporter analysis was supported by grants AGL2011-29925 and AGL2015-66131- AGL2015-66131-C2-2-R (MINECO/FEDER).

Published
2017
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2. Competitive actions of MnSi in the epitaxial growth of Mn5Si3 thin films on Si(111)

Author

Kounta, Ismaïla, Reichlova, Helena, Kriegner, Dominik, Lopes Seeger, Rafael, Bad'Ura, Antonin, Leiviska, Miina, Boussadi, Amine, Heresanu, Vasile, Bertaina, Sylvain, Petit, Matthieu, Schmoranzerova, Eva, Smejkal, Libor, Sinova, Jairo, Jungwirth, Tomas, Baltz, Vincent, Goennenwein, Sebastian, Michez, Lisa, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut für Festkörper- und Materialphysik, Technische Universität Dresden, Technische Universität Dresden = Dresden University of Technology (TU Dresden), Dresden-Würzburg Center of Excellence on Complexity and Topology in Quantum Matte (ct.qmat), Institute of Physics of the Czech Academy of Sciences (FZU / CAS), Czech Academy of Sciences [Prague] (CAS), SPINtronique et TEchnologie des Composants (SPINTEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Faculty of Mathematics and Physics [Charles University of Praha], Charles University [Prague] (CU), Institut des Matériaux, de Microélectronique et des Nanosciences de Provence (IM2NP), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), Institut für Physik Johannes Gutenberg Universität, Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), School of Physics and Astronomy, University of Nottingham, Fachbereich Physik, Universität Konstanz, Universitätsstraße 10, D-78453 Konstanz, Germany ( Fachbereich Physik, Universität Konstanz), Fachbereich Physik, Universität Konstanz, GACR Grant No. 22-17899K, Lumina Quaeruntur fellowship of the Czech Academy of Science (Grant No. LQ100102201), Elasto-Q-Mat (DFG SFB TRR 288), and ANR-20-CE92-0049,MATHEEIAS,Effets magnéto-thermo-électriques en électronique de spin antiferromagnétique(2020)

Subjects
Mn5Si3, Antiferromagnetism, Interface & surface thermodynamics, Anomalous hall effect, MBE - Molecular Beam Epitaxy, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Spintronics
Abstract

International audience; Some magnetically ordered phases of the Mn5Si3 crystal are proving to be prototypes for the study of thenew fundamental spin physics related to the spontaneous breaking of the time-reversal symmetry despite a zeronet magnetization. Here, we report on a route to grow epitaxial Mn5Si3 thin films on Si(111). To this end, weuse Mn and Si codeposition in a molecular beam epitaxy system and carefully tune the deposition rates, thegrowth temperature, and the annealing temperature. We assessed the silicide phase-formation and morphologyusing reflection high-energy electron diffraction, x-ray diffraction, high-resolution transmission electron mi-croscopy (HRTEM) and atomic force microscopy. Layers containing only Mn5Si3 could be stabilized undervery restrictive conditions, by tuning the Mn/Si flux ratio to match the compound stoichiometry and adjustingthe substrate temperature during growth to 443 K. HRTEM imaging revealed the existence of an interfacialamorphous layer of few nanometers thickness. Annealing the heterostructure up to 573 K led to the formationof MnSi at the vicinity of the Mn5Si3/Si(111) interface, which significantly reduced the nucleation barrier ofMn5Si3. High-quality crystalline Mn5Si3 thin films were then formed with the following epitaxial relationships:Mn5Si3 (0001)[011̄0]//MnSi(111)[2̄11]//Si(111)[11̄0]. Our experiments showed that the formation of MnSi isenhanced at a growth temperature above 473 K or for a longer annealing step, while the crystalline quality of theMn5Si3 overlayer is correspondingly degraded leading to textured thin films. The growth pathways and structuralproperties of the manganese silicides can be rationalized in terms of reactions maximizing the free-energylowering rate. Moreover, we found that the magnetic and the magnetotransport properties can be used as anefficient tool to track both Mn5Si3 crystallinity and proportion in the deposited layers.

Published
2023
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3. Intégration hétérogène pour la mise en œuvre de capteurs imprimés sur support souple connectés

Author

Vauche, Rémy, Benevent, Evangéline, Moindje, Soilihi, Walder, Jean-Pierre, Blalta, Yacine, Bouchnak, Katrinada, Khelladi, Hajar, Nuon, Sochanshakhéna, Institut des Matériaux, de Microélectronique et des Nanosciences de Provence (IM2NP), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), and IUT d'Aix-Marseille

Subjects
intégration hétérogène, Bluetooth Low Energy, [INFO]Computer Science [cs], [INFO.EIAH]Computer Science [cs]/Technology for Human Learning, capteur connecté, capteur imprimé, capteur sur support souple
Abstract

International audience; Cet article présente les résultats obtenus lors de la première édition d’un projet étudiant réalisé par des étu-diants en 3ième année du cycle ingénieur du département Micro-électronique et Télécommunications de Polytech’ Mar-seille au cours du premier semestre de l’année scolaire 2020-2021. Ce projet a été proposé dans le cadre l’action transverseIntégration Hétérogène du laboratoire IM2NP qui vise à développer à terme avec le support de la plate-forme IO LAB del’IM2NP, une plate-forme de démonstration connectée et alimentée sur batterie de capteurs imprimés sur support souple,l’objectif final étant de mettre en avant le savoir-faire qui a été acquis par la plate-forme SPRINT de l’IM2NP en matièrede conception et de fabrication de capteurs sur support souple. Le standard de communications sans-fil retenu pour cedémonstrateur est le Bluetooth Low Energy (BLE) afin de permettre l’affichage des données issues d’un capteur sur undispositif mobile compatible telles qu’une tablette ou un smartphone. Il sera ici mis en œuvre à l’aide du moduleBlueNRG-M2SP de chez STMicroelectronics qui, en plus d’avoir un faible encombrement, dispose d’un Cortex M0,d’une mémoire Flash programmable ainsi qu’un Convertisseur Analogique-Numérique (CAN), lui permettant ainsi d’êtreutilisé seul, sans qu’aucun composant additionnel ne soit nécessaire. Néanmoins, devant les difficultés rencontrées parles étudiants pour développer en autonomie une application personnalisée dédiée à ce module, il a été programmé avecun microcode fourni par STMicroelectronics et contrôlé en SPI par un autre microcontrôleur possédant un CAN pourarriver au résultat attendu

Published
2021

4. Using Whole Document Context in Neural Machine Translation

Author

Mac��, Valentin, Servan, Christophe, QWANT RESEARCH (QR), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), and Servan, Christophe

Subjects
FOS: Computer and information sciences, [INFO.INFO-TT]Computer Science [cs]/Document and Text Processing, Computer Science - Computation and Language, [INFO.INFO-CL] Computer Science [cs]/Computation and Language [cs.CL], ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, [INFO.INFO-TT] Computer Science [cs]/Document and Text Processing, Computation and Language (cs.CL), [INFO.INFO-CL]Computer Science [cs]/Computation and Language [cs.CL]
Abstract

In Machine Translation, considering the document as a whole can help to resolve ambiguities and inconsistencies. In this paper, we propose a simple yet promising approach to add contextual information in Neural Machine Translation. We present a method to add source context that capture the whole document with accurate boundaries, taking every word into account. We provide this additional information to a Transformer model and study the impact of our method on three language pairs. The proposed approach obtains promising results in the English-German, English-French and French-English document-level translation tasks. We observe interesting cross-sentential behaviors where the model learns to use document-level information to improve translation coherence., Accepted paper to IWSLT2019

Published
2019

5. Optoelectronical-based multiplexed transmission of analog signals in a magnetic environment

Author

Vilmen, Christophe, Bortoli, Louis, Gallouin, Evan, Guye, Maxime, Bernard, Monique, David, Bendahan, Fouré, Alexandre, Centre de résonance magnétique biologique et médicale (CRMBM), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), ESTIA INSTITUTE OF TECHNOLOGY, Centre d'Exploration Métabolique par Résonance Magnétique [Hôpital de la Timone - APHM] (CEMEREM), Hôpital de la Timone [CHU - APHM] (TIMONE)-Centre de résonance magnétique biologique et médicale (CRMBM), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Centre National de la Recherche Scientifique (CNRS), and International Society for Magnetic Resonance in Medicine

Subjects
[SPI]Engineering Sciences [physics], [SDV]Life Sciences [q-bio]
Abstract

IntroductionThe assessment of activation and energetics in exercising muscle has been abundantly performed in high field magnetic environment1-3 using MR imaging (MRI) and 31P spectroscopy (31P-MRS). In order to control and measure exercise intensity, dedicated MR-compatible ergometers have been built4-6 and kinetic parameters of the movement have been assayed with specific sensors. For most of the setups reported so far, signals were transmitted with wires7,8 related to potential risks of electromagnetic interferences (EMI). More recently and with the aim of limiting EMI, a research group reported the utilization of an optical sensor9 which can be directly transmitted with an optical fiber where other used the conversion of analog signal from a conventional sensor to an optical transmission.5,10 However, these kinds of setup have never been designed for multiple sensors in order to assess multiple kinetic parameters leading to an accurate quantification of muscular work during exercise.In the present study, we report results related to an original setup allowing a multiplexed optical transmission of signals from multiple analog sensors connected to MR-compatible ergometer. We demonstrated that multiple analog signals can be simultaneously transmitted via a single optical fiber.MethodsTwo communication units connected by an optical fiber were designed to convert and transmit analog signals measured by sensors connected to a MR-compatible ergometer previously described.6 A schematic representation of the experimental design is displayed in Figure 1. Briefly, the unit in the MR scanner room digitally encodes the different analogic signals (forces, displacements and angle) and converts them into a multiplexed code using an Arduino-based microcontroller. Then the composite signal is transmitted (Steps #1 and #2) via a single optical fiber (Step #3) to the second unit located inside the control room. The second unit handles the composite signal demultiplexing and the digital-to-analog conversion, using another Arduino-based microcontroller (Steps #4).In order to assess the accuracy of our measurements, we compared the analog signals at the sensors level and those from the output transducer. The corresponding results were analyzed with a Pearson product-moment correlation (r). A linear adjustment (calibration) between the electric signal and the calibrated measures was assessed with a determination coefficient R2.Analog signals were recorded during a 31P-MRS investigation performed in a single subject in a 3T super-conducting whole-body scanner (Siemens Verio, Erlangen, Germany). A 31P-1H surface coil was positioned under the right quadriceps femoris muscle group. Fully-relaxed (TR = 15s, NEX = 1, Number of Scans = 6) 31P spectra were recorded at rest while analog signals were measured during a submaximal exercise. The signal-to-noise (SNR) of 31P spectra and the PCr/ATP ratios were quantified.ResultsThe correlations between analog signals measured on both sides of the optical transmission were very high (r > 0.99, Figure 2). The very high determination coefficients found for each channel (R² > 0.99) supported the accuracy of the corresponding measurements (Figure 2).The SNR of the 31P MR spectra was very large (93 ± 9) while the averaged of PCr/ATP value was 3.9 ± 0.5 (Figure 4).DiscussionWe designed an optical-based electronic device which allowed accurate and reliable analog measurements in a magnetic environment. Shape and amplitude of mechanical signals were similar to those obtained in previous studies.6,11 The SNR of the 31P MR spectra and the metabolic ratio were also in accordance with those previously reported.12,13 In addition, our system considerably reduced wires congestion and potential electric/magnetic signal crosstalk. No mutual influence of the electric and magnetic signals was found thereby demonstrating the ability of our system to assess mechanical parameters in exercising muscle within a magnetic environment.ConclusionOur electronic device based on a multiplexed transmission via an optical fiber allows an accurate conversion/transmission of several analog signals related to human movement kinetics and measured in a high-field magnetic environment.

Published
2018

6. Estimating single molecule conductance from spontaneous evolution of a molecular contact

Author

M. Gil, M. Iazykov, T. Malinowski, Hubert Klein, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), and ANR-12-BS10-0018,FOST,Dispositif moléculaire à 4 états(2012)

Subjects
Thermal equilibrium, [PHYS]Physics [physics], Materials science, Molecular electronic, Condensed Matter - Mesoscale and Nanoscale Physics, General Physics and Astronomy, Molecular electronics, Conductance, FOS: Physical sciences, 02 engineering and technology, Conductivity, 010402 general chemistry, 021001 nanoscience & nanotechnology, Thermal diffusivity, 01 natural sciences, Molecular physics, 0104 chemical sciences, Single molecule conductance, Break junction, Electrode, Mesoscale and Nanoscale Physics (cond-mat.mes-hall), Molecule, 0210 nano-technology
Abstract

We present an original method to estimate the conductivity of a single molecule anchored to nanometric-sized metallic electrodes, using a Mechanically Controlled Break Junction (MCBJ) operated at room temperature in liquid. We record the conductance through the metal / molecules / metal nanocontact while keeping the metallic electrodes at a fixed distance. Taking advantage of thermal diffusion and electromigration, we let the contact naturally explore the more stable configurations around a chosen conductance value. The conductance of a single molecule is estimated from a statistical analysis of raw conductance and conductance standard deviation data for molecular contacts containing up to 14 molecules. The single molecule conductance values are interpreted as time-averaged conductance of an ensemble of conformers at thermal equilibrium., 25 pages, 6 figures

Published
2018
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7. Regular paper Review of Different MPPT techniques for a Photovoltaic Generation System

Author

Kchaou, Ameni, Naamane, A, Koubaa, Y, M'Sirdi, N., École Nationale d'Ingénieurs de Sfax | National School of Engineers of Sfax (ENIS), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), and M'Sirdi, Kouider Nacer

Subjects
[SPI.AUTO] Engineering Sciences [physics]/Automatic, Maximum Power Point Tracking (MPPT), Photovoltaic System, [SPI.AUTO]Engineering Sciences [physics]/Automatic
Abstract

International audience; The Photovoltaic (PV) panel characteristic is nonlinear and depends on solar irradiation and temperature cell variation. Consequently, a Maximum Power Point Tracking (MPPT) algorithm is necessary to obtain the maximized produced energy from the PV. The main purpose of MPPT technique is to guarantee that the maximum power is produced. This allows to extract the maximum power instantaneously. This paper is aimed to study the performance of different MPPT techniques. These techniques are tested while the temperature was randomly varied. The simulation results are evaluated via Matlab-Simulink.

Published
2017

8. Versatile synthesis of tunable N,S-bridged-[1.1.1.1]-cyclophanes promoted by ester functions

Author

Olivier Siri, Vinícius Demétrio da Silva, Michel Giorgi, Volodymyr Malytskyi, Jean-Manuel Raimundo, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Spectropôle - Aix Marseille Université (AMU SPEC), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Scope (project management), 010405 organic chemistry, Chemistry, [1.1.1.1]-Cyclophanes, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Organic Chemistry, Organic synthesis, 010402 general chemistry, 01 natural sciences, Biochemistry, Combinatorial chemistry, SNAr, 0104 chemical sciences, chemistry.chemical_compound, Nucleophilic aromatic substitution, Drug Discovery, Organic chemistry, [CHIM]Chemical Sciences, Solubility, Macrocycles
Abstract

International audience; We report herein a powerful and highly adaptable metal-free organic synthetic route to functionalized N,S-bridged-[1.1.1.1]-cyclophanes using an ester-promoted macrocyclisation step. The newly synthesized cyclophanes are obtained in good yields exhibiting (i) high solubility, allowing the possibility to enlarge the scope and chemistry for such macrocycles, (ii) a tunable cavity and (iii) orthogonal functional groups. (C) 2016 Elsevier Ltd. All rights reserved.

Published
2016
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9. Importing cooperative pedagogy into postgraduate courses - an experiment

Author

Bac, Alexandra, Ben-Miloud, Alexis, Rozo-Brezillac, Axel, Aix Marseille Université (AMU), Polytech Marseille (AMU POLYTECH), and Bac, Alexandra

Subjects
Pedagogy, [SHS.EDU]Humanities and Social Sciences/Education, [SHS.EDU] Humanities and Social Sciences/Education, Higher education, Cooperative pedagogy, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

10. Exudate production : a detoxification strategy of wood decaying fungi

Author

Deroy, Aurélie, Berrin, Jean-Guy, Dumarcay, Stéphane, Gerardin, Philippe, Kohler, Annegret, Navarro, D, Rose, C, Sormani, Rodnay, MOREL-ROUHIER, Melanie, Gelhaye, Eric, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Biodiversité et Biotechnologie Fongiques (BBF), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Laboratoire d'Etude et de Recherche sur le Matériau Bois (LERMAB), Université de Lorraine (UL), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), and École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)

Subjects
secretome, [SDV]Life Sciences [q-bio], Trametes versicolor, exudate, detoxification
Abstract

International audience; Even often observed, the exudate production in fungi remains mainly unstudied. During growth on oak wood, the white-rot fungus Trametes versicolor produces droplets of a red-brown liquid, this phenomenom being observed with nine studied strains. One of these strains secretes a similar exudate on rich medium even in the absence of wood. This secretion seems to be linked to the formation of special fungal structures involved in the production of extracellular enzymes. A proteomic study revealed that the protein content of the exudate is indeed closely related to extracellular enzymatic systems secreted by Trametes versicolor during oak degradation. It contains in particular enzymes involved in aromatic compounds oxidation such as Dye peroxidase, versatile and manganese peroxidases and also various carbohydrate-active enzymes. The proteomic studies revealed also the presence of a detoxification system involving glutathione related systems. In addition, a transcriptomic approach showed that this process is linked to induction of genes involved in intracellular degradation and detoxification of wood extractives and reactive oxygen species. From these observations, we propose that such exudate production by pioneer wood colonizers such as Trametes versicolor could be a way for facilitating extraction, concentration and degradation of wood extractives and other potential toxic by-products produced during the wood degradation oxidative process.

Published
2016

11. Subpicomolar Iron Sensing Platform Based on Functional Lipid Monolayer Microarrays

Author

Anne Charrier, Tuyen D. Nguyen, H. Dallaporta, Jean-Manuel Raimundo, Ahmad Kenaan, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), and Aix Marseille Université (AMU)

Subjects
Silicon, Iron, chemistry.chemical_element, Nanotechnology, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Analytical Chemistry, Diynes, Limit of Detection, Monolayer, Microscopy, [CHIM]Chemical Sciences, Lithography, Detection limit, Kelvin probe force microscope, Membranes, Artificial, Lipid monolayer, 021001 nanoscience & nanotechnology, Microarray Analysis, 0104 chemical sciences, chemistry, Pyrones, Phosphatidylcholines, DNA microarray, 0210 nano-technology
Abstract

International audience; We report herein the fabrication of novel micro-arrays based on air-stable functional lipid monolayers over silicon using a combination of e-beam lithography and lift-off. We demonstrate these microarrays can be use as ultrasensitive platform for Kelvin probe force microscopy in sensing experiments. Specificity of the detection is given by the functional group grafted at the lipid headgroup. The arrays developed for the detection of ferric ions, Fe3+, using a gamma-pyrone derivative chelator, demonstrate subpicomolar limit of detection with high specificity. In addition, the technique takes advantage of the structure of the array with the silicon areas playing the role of reference for the measurement, and we determine critical pattern dimensions below which the probe size/shape impacts the measured results.

Published
2016
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12. Electrical and optical measurements of the bandgap energy of a light-emitting diode

Author

Lisa Michez, Philippe Dumas, Jean-Manuel Raimundo, Matthieu Petit, Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Work (thermodynamics), Band gap, Optical measurements, General Physics and Astronomy, p-n junctions, semiconductors, 01 natural sciences, Education, law.invention, law, 0103 physical sciences, Electronics, 010306 general physics, Diode, Physics, business.industry, 05 social sciences, LED, 050301 education, bandgap, Semiconductor, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Optoelectronics, light-emitting diode, business, 0503 education, Energy (signal processing), Light-emitting diode
Abstract

International audience; Semiconductors materials are at the basis of electronics. Most electronic devices are made of semiconductors. The operation of these components is well described by quantum physics which is a little mysterious to students. One of the intrinsic parameters of semiconductors is their bandgap energy Eg. In the case of light-emitting diodes (LEDs) Eg fixes the colour of the light emitted by the diodes. We propose in this article a lab work allowing a comparison of Eg of a green LED obtained by both electrical and optical measurements. The two slightly different results can be explained by the theoritical knowledges of the students on solid physics and electronic devices internal architecture.

Published
2016
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13. Single-domain flavoenzymes trigger lytic polysaccharide monooxygenases for oxidative degradation of cellulose

Author

Mathieu Fanuel, Frédéric Biaso, Eric Record, David Ropartz, Sona Garajova, Jean-Guy Berrin, Chloé Bennati-Granier, Hélène Rogniaux, Bernard Henrissat, Bruno Guigliarelli, Yann Mathieu, Maria Rosa Beccia, Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Biodiversité et Biotechnologie Fongiques (BBF), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Bioénergétique et Ingénierie des Protéines (BIP ), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Dipartimento di Chimica e Chimica Industriale, Università di Pisa, INRA Plateforme BIBS, Unité de Recherche Biopolymères, Interactions, Assemblages, Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), King Abdulaziz University, AMIDEX foundation (Funcopper project) [A*M-AAP-EI-13-13-130115-15.37, ANR-11-IDEX-0001-02], INDOX European project [FP7-KBBE-2013-7-613549], ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), European Project: 613549,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,INDOX(2013), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Berrin, Jean-Guy, École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and ANR-11-IDEX-0001-02/11-IDEX-0001,AMIDEX,AMIDEX(2011)

Subjects
0301 basic medicine, Cellobiose dehydrogenase, crassa electron-transfer, Oxidative phosphorylation, Cellobiose, ustilago-maydis, Biology, Polysaccharide, Article, Mixed Function Oxygenases, Fungal Proteins, 03 medical and health sciences, chemistry.chemical_compound, Protein Domains, Podospora, Glucose dehydrogenase, Cellulose, cellobiose dehydrogenase, mono-oxygenases, chemistry.chemical_classification, Multidisciplinary, Vegetal Biology, Flavoproteins, fungus pycnoporus-cinnabarinus, podospora-anserina, phanerochaete-chrysosporium, substrate-specificity, neurospora, biomass, Monooxygenase, 030104 developmental biology, Enzyme, [CHIM.POLY]Chemical Sciences/Polymers, chemistry, Biochemistry, Carbohydrate Dehydrogenases, Biologie végétale
Abstract

The enzymatic conversion of plant biomass has been recently revolutionized by the discovery of lytic polysaccharide monooxygenases (LPMOs) that carry out oxidative cleavage of polysaccharides. These very powerful enzymes are abundant in fungal saprotrophs. LPMOs require activation by electrons that can be provided by cellobiose dehydrogenases (CDHs), but as some fungi lack CDH-encoding genes, other recycling enzymes must exist. We investigated the ability of AA3_2 flavoenzymes secreted under lignocellulolytic conditions to trigger oxidative cellulose degradation by AA9 LPMOs. Among the flavoenzymes tested, we show that glucose dehydrogenase and aryl-alcohol quinone oxidoreductases are catalytically efficient electron donors for LPMOs. These single-domain flavoenzymes display redox potentials compatible with electron transfer between partners. Our findings extend the array of enzymes which regulate the oxidative degradation of cellulose by lignocellulolytic fungi.

Published
2016
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14. Recombinant protein production facility for fungal biomass-degrading enzymes using the yeast Pichia pastoris

Author

Jean-Guy Berrin, Antoine Gruet, David Navarro, Christophe Bignon, Mireille Haon, Sacha Grisel, Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-École Centrale de Marseille (ECM), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Laboratory of Protein and Nucleic Acid Chemistry, Rockefeller University [New York], Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), French National Research Agency [ANR FUNLOCK ANR13-BIME-0002-01], École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), The Rockefeller University, Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Berrin, Jean-Guy, Bignon, Christophe, and Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)

Subjects
Microbiology (medical), analyse factorielle, lcsh:QR1-502, Computational biology, Molecular cloning, Microbiology, recombinant proteins, lcsh:Microbiology, Pichia pastoris, law.invention, factorial approach, law, Methods, Glycoside hydrolase, glycoside hydrolase, antigène recombinant, automation, chemistry.chemical_classification, expression platform, CAZymes, biology, biology.organism_classification, Yeast, Fungal biomass, Transformation (genetics), Enzyme, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Recombinant DNA, automatisation
Abstract

International audience; Filamentous fungi are the predominant source of lignocellulolytic enzymes used in industry for the transformation of plant biomass into high-value molecules and biofuels. The rapidity with which new fungal genomic and post-genomic data are being produced is vastly outpacing functional studies. This underscores the critical need for developing platforms dedicated to the recombinant expression of enzymes lacking confident functional annotation, a prerequisite to their functional and structural study. In the last decade, the yeast Pichia pastoris has become increasingly popular as a host for the production of fungal biomass-degrading enzymes, and particularly carbohydrate-active enzymes (CAZymes). This study aimed at setting-up a platform to easily and quickly screen the extracellular expression of biomass-degrading enzymes in P. pastoris. We first used three fungal glycoside hydrolases (GHs) that we previously expressed using the protocol devised by Invitrogen to try different modifications of the original protocol. Considering the gain in time and convenience provided by the new protocol, we used it as basis to setup the facility and produce a suite of fungal CAZymes (GHs, carbohydrate esterases and auxiliary activity enzyme families) out of which more than 70% were successfully expressed. The platform tasks range from gene cloning to automated protein purifications and activity tests, and is open to the CAZyme users' community.

Published
2015
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15. Substrate specificity and regioselectivity of fungal AA9 lytic polysaccharide monooxygenases secreted by Podospora anserina

Author

Charlotte Champion, Simeng Zhou, Jean-Guy Berrin, Eric Record, Hélène Rogniaux, Mathieu Fanuel, Mireille Haon, Sacha Grisel, Chloé Bennati-Granier, Sona Garajova, David Ropartz, Isabelle Gimbert, Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-École Centrale de Marseille (ECM), Institute of Chemistry, Slovakian Academy of sciences, INRA Plateforme BIBS, Unité de Recherche Biopolymères, Interactions, Assemblages, École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Berrin, Jean-Guy, Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), and Institut National de la Recherche Agronomique (INRA)

Subjects
dégradation de la biomasse, CELLOBIOSE DEHYDROGENASE, CELLULOSE DEGRADATION, Applied Microbiology and Biotechnology, Podospora anserina, dégradation enzymatique, LIGNOCELLULOSIC BIOMASS, AA9, SACCHARIFICATION, LPMO, Biomass, Trichoderma reesei, chemistry.chemical_classification, 0303 health sciences, biology, Biologie du développement, monooxygénase, Development Biology, Oxidized cello-oligosaccharides, FAMILY, TRICHODERMA-REESEI, OLIGOSACCHARIDES, General Energy, Biochemistry, Lytic cycle, champignon ascomycete, Lignocellulose, ENZYMES, Biotechnology, Research Article, Cellobiose dehydrogenase, hémicellulose, Management, Monitoring, Policy and Law, Oxidative cleavage, Polysaccharide, Microbiology, Neurospora crassa, 03 medical and health sciences, Biorefinery, Cellulose, Hemicellulose, podospora anserina, NEUROSPORA-CRASSA, 030304 developmental biology, 030306 microbiology, Renewable Energy, Sustainability and the Environment, Monooxygenase, biology.organism_classification, champignon filamenteux, Enzyme, PICHIA-PASTORIS, chemistry, cellobiose déshydrogénase, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

Background The understanding of enzymatic polysaccharide degradation has progressed intensely in the past few years with the identification of a new class of fungal-secreted enzymes, the lytic polysaccharide monooxygenases (LPMOs) that enhance cellulose conversion. In the fungal kingdom, saprotrophic fungi display a high number of genes encoding LPMOs from family AA9 but the functional relevance of this redundancy is not fully understood. Results In this study, we investigated a set of AA9 LPMOs identified in the secretomes of the coprophilous ascomycete Podospora anserina, a biomass degrader of recalcitrant substrates. Their activity was assayed on cellulose in synergy with the cellobiose dehydrogenase from the same organism. We showed that the total release of oxidized oligosaccharides from cellulose was higher for PaLPMO9A, PaLPMO9E, and PaLPMO9H that harbored a carbohydrate-binding module from the family CBM1. Investigation of their regioselective mode of action revealed that PaLPMO9A and PaLPMO9H oxidatively cleaved at both C1 and C4 positions while PaLPMO9E released only C1-oxidized products. Rapid cleavage of cellulose was observed using PaLPMO9H that was the most versatile in terms of substrate specificity as it also displayed activity on cello-oligosaccharides and β-(1,4)-linked hemicellulose polysaccharides (e.g., xyloglucan, glucomannan). Conclusions This study provides insights into the mode of cleavage and substrate specificities of fungal AA9 LPMOs that will facilitate their application for the development of future biorefineries. Electronic supplementary material The online version of this article (doi:10.1186/s13068-015-0274-3) contains supplementary material, which is available to authorized users.

Published
2015
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16. Essential oils and distilled straws of lavender and lavandin: a review of current use and potential application in white biotechnology

Author

Marine Bou, Jean-Claude Sigoillot, Craig B. Faulds, Anne Lomascolo, Laurence Lesage-Meessen, Biodiversité et Biotechnologie Fongiques (BBF), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), FranceAgrimer Institute (Etablissement National des Produits de l'Agriculture et de la Mer, Paris, France), French Pole of Competitiveness Parfums Aromes Senteurs Saveurs (Grasse, France), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), and Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-École Centrale de Marseille (ECM)

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, Lavender, Lavandula, ANGUSTIFOLIA, AROMATIC PLANTS, Lavandin, ASPERGILLUS-NIGER, Linalyl acetate, CHEMICAL-COMPOSITION, ANTIFUNGAL ACTIVITY, Applied Microbiology and Biotechnology, law.invention, Terpene, Steam distillation, chemistry.chemical_compound, Linalool, law, Bioproducts, Oils, Volatile, Humans, Plant Oils, Distillation, Lavandula angustifolia, Plant Stems, business.industry, Terpenes, Biotechnological application, food and beverages, Distilled straws, General Medicine, IN-VITRO, Biotechnology, chemistry, PYCNOPORUS-CINNABARINUS, HARVEST TIME, Phenolics, X-INTERMEDIA, business, ANTIOXIDANT ACTIVITY
Abstract

The Lavandula genus, which includes lavender (Lavandula angustifolia) and lavandin (L. angustifolia x Lavandula latifolia), is cultivated worldwide for its essential oils, which find applications in perfumes, cosmetics, food processing and, more recently, in aromatherapy products. The chemical composition of lavender and lavandin essential oils, usually produced by steam distillation from the flowering stems, is characterized by the presence of terpenes (e.g. linalool and linalyl acetate) and terpenoids (e.g. 1,8-cineole), which are mainly responsible for their characteristic flavour and their biological and therapeutic properties. Lavender and lavandin distilled straws, the by-products of oil extraction, were traditionally used for soil replenishment or converted to a fuel source. They are mineral- and carbon-rich plant residues and, therefore, a cheap, readily available source of valuable substances of industrial interest, especially aroma and antioxidants (e.g. terpenoids, lactones and phenolic compounds including coumarin, herniarin, alpha-bisabolol, rosmarinic and chlorogenic acids). Accordingly, recent studies have emphasized the possible uses of lavender and lavandin straws in fermentative or enzymatic processes involving various microorganisms, especially filamentous fungi, for the production of antimicrobials, antioxidants and other bioproducts with pharmaceutical and cosmetic activities, opening up new challenging perspectives in white biotechnology applications.

Published
2015
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17. Wireless Holons Network for Intralogistics Service

Author

Fouzia Ounnar, Tarik Remous, Patrick Pujo, Centre de Recherche sur le Transport et la Logistique (CRET-LOG), Aix Marseille Université (AMU), Polytech Marseille (AMU POLYTECH), and T Borangiu et al

Subjects
Flexibility (engineering), Service (systems architecture), business.industry, Job shop, Computer science, 020208 electrical & electronic engineering, Control (management), 02 engineering and technology, Manufacturing systems, 020202 computer hardware & architecture, Engineering management, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, 0202 electrical engineering, electronic engineering, information engineering, Wireless, Production (economics), [INFO.INFO-RB]Computer Science [cs]/Robotics [cs.RO], business, Intelligent control, ComputingMilieux_MISCELLANEOUS, Computer network
Abstract

This paper continues our previous research works on holonic and isoarchic control solution for manufacturing systems control based on the PROSIS model, this time considering WSN technology as support for new opportunities of flexibility, security and performance for production systems. First, the objectives are addressed. The WSN technology allows the association of a decision-making capacity to each physical entity of the production system. An application to an intralogistics service in a Job Shop is presented. New opportunities for intelligent control of production systems are highlighted.

Published
2015
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18. Clogging of microporous channels networks: role of connectivity and tortuosity

Author

Patrice Bacchin, K. Glucina, Damien Veyret, Quentin Derekx, Philippe Moulin, Laboratoire de génie chimique [ancien site de Basso-Cambo] (LGC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Mécanique, Modélisation et Procédés Propres (M2P2), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Suez Environnement, Centre International de Recherche Sur l'Eau et l'Environnement (CIRSEE), Aix-Marseille Université - AMU (FRANCE), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Polytech'Marseille (FRANCE), SUEZ ENVIRONNEMENT (FRANCE), Laboratoire de Génie Chimique (LGC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), and Institut National Polytechnique de Toulouse - INPT (FRANCE)

Subjects
Plugging, Materials science, Computer simulation, Microfluidics, Video microscopy, Nanotechnology, Mechanics, Numerical simulation, Fouling, Condensed Matter Physics, Tortuosity, Electronic, Optical and Magnetic Materials, law.invention, Clogging, Microchannels, law, Materials Chemistry, Particle, Génie chimique, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Porous medium, Génie des procédés, Filtration
Abstract

The aim of this work is to study the pore blocking by the use of microfluidic devices (micro-separators) and numerical simulation approaches. The micro-separators are made in PDMS and are constituted of an array of microchannels 20 micrometers wide with three types of structure: straight microchannels, connected microchannels (or aligned square pillars) and staggered square pillars in order to mimic merely the complexity of the flow encountered in filters or membranes (tortuosity, connectivity between pores). Direct observation with video microscopy of filtrations of 5 micrometers latex particles has been performed to examine the capture of particles. The results show a piling up of particles within the porous media leading to a clogging. The capture efficiency remains low (less than 0.1%). In the case of filtration in the forest of pillars, the capture is faster and arises mainly between the pillars. The increase in tortuosity in the micro-separator leads then to a rise of the clogging. It must be caused by the increase in critical trajectories leading to the capture of particles on the PDMS walls. At the same time, numerical simulations of filtration in parallel with microchannels have been performed in the same flow conditions with GeoDict software. The different kind of experimental deposit structure can be simulated but there is still inaccuracy in the description of the accumulation kinetics. These discrepancies are probably due to the lack of accuracy to depict particle/particle colloidal interactions in simulations and the fact that re-suspension of particles after capture is not well described.

Published
2014
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19. Integrative analysis of the transcriptome profiles observed in type 1, type 2 and gestational diabetes mellitus reveals the role of inflammation

Author

Cristhianna A V Collares, Milton César Foss, Elza Tiemi Sakamoto-Hojo, Fernanda S. Manoel-Caetano, Denis Puthier, Diane M. Rassi, Geraldo Aleixo Silva Passos, Catherine Nguyen, Danilo J. Xavier, Maria Cristina Foss-Freitas, Adriane Feijó Evangelista, Claudia Macedo, Eduardo Antônio Donadi, Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), and Aix Marseille Université (AMU)

Subjects
Male, endocrine system diseases, Genome-wide association study, Module map, Type 2 diabetes, Bioinformatics, Transcriptome, 0302 clinical medicine, Pregnancy, Cluster Analysis, Genetics(clinical), Genetics (clinical), Gestational diabetes, Oligonucleotide Array Sequence Analysis, 0303 health sciences, Principal Component Analysis, Reverse Transcriptase Polymerase Chain Reaction, Middle Aged, Markov Chains, 3. Good health, Type 1 diabetes, 030220 oncology & carcinogenesis, Female, Transcriptome analysis, Algorithms, Research Article, Adult, Adolescent, INFLAMAÇÃO, Biology, Real-Time Polymerase Chain Reaction, 03 medical and health sciences, Young Adult, Diabetes mellitus, medicine, Genetics, Humans, 030304 developmental biology, Rank product, Aged, Demography, Inflammation, Gene Expression Profiling, Reproducibility of Results, nutritional and metabolic diseases, Immune cell signatures, medicine.disease, Gene expression profiling, Diabetes, Gestational, Diabetes Mellitus, Type 1, Diabetes Mellitus, Type 2, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

Background Type 1 diabetes (T1D) is an autoimmune disease, while type 2 (T2D) and gestational diabetes (GDM) are considered metabolic disturbances. In a previous study evaluating the transcript profiling of peripheral mononuclear blood cells obtained from T1D, T2D and GDM patients we showed that the gene profile of T1D patients was closer to GDM than to T2D. To understand the influence of demographical, clinical, laboratory, pathogenetic and treatment features on the diabetes transcript profiling, we performed an analysis integrating these features with the gene expression profiles of the annotated genes included in databases containing information regarding GWAS and immune cell expression signatures. Methods Samples from 56 (19 T1D, 20 T2D, and 17 GDM) patients were hybridized to whole genome one-color Agilent 4x44k microarrays. Non-informative genes were filtered by partitioning, and differentially expressed genes were obtained by rank product analysis. Functional analyses were carried out using the DAVID database, and module maps were constructed using the Genomica tool. Results The functional analyses were able to discriminate between T1D and GDM patients based on genes involved in inflammation. Module maps of differentially expressed genes revealed that modulated genes: i) exhibited transcription profiles typical of macrophage and dendritic cells; ii) had been previously associated with diabetic complications by association and by meta-analysis studies, and iii) were influenced by disease duration, obesity, number of gestations, glucose serum levels and the use of medications, such as metformin. Conclusion This is the first module map study to show the influence of epidemiological, clinical, laboratory, immunopathogenic and treatment features on the transcription profiles of T1D, T2D and GDM patients.

Published
2014
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20. Wiresless Control Network for Intralogistics Service in a Holonic and Isoarchic Control Approach

Author

Pujo, Patrick, Ounnar, Fouzia, Remous, Tarik, Centre de Recherche sur le Transport et la Logistique (CRET-LOG), Aix Marseille Université (AMU), and Polytech Marseille (AMU POLYTECH)

Subjects
[INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, [INFO.INFO-RB]Computer Science [cs]/Robotics [cs.RO]
Abstract

International audience; This paper continues our previous research works on holonic and isoarchic control solution for manufacturing systems control based on the PROSIS model, this time considering WSN technology as support for new opportuni-ties of flexibility, security and performance for production systems. First, the objectives are addressed. The WSN technology allows the association of a decision-making capacity to each physical entity of the production system. An application to an intralogistics service in a Job Shop is presented. New opportunities for intelligent control of production systems are highlighted.

Published
2014

21. [Functions of lncRNA in development and diseases]

Author

Mathieu, E. L., Belhocine, M., Dao, L. T., Puthier, Denis, Spicuglia, S., Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

International audience; The transcription of essentially the entire eukaryotic genome generates a myriad of non-coding RNA species that show complex overlapping patterns of expression and regulation. In the last decade, several large scale genomic analyses have shed light on the widespread existence of long non-coding RNAs (lncRNAs) in mammals. Although the function of most lncRNAs remains unknown, many of them have been suggested to play important roles in the regulation of gene expression during normal development and diseases, including cancers. Indeed, functional studies have demonstrated that lncRNAs participate in various biological processes, including reprogramming of pluripotent stem cells, oncogenic progression and cell cycle regulation. In this review, we summarize recent findings about the biology of lncRNAs and their functions in normal and pathological development in mammals.

Published
2014
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22. Divergent transcription is associated with promoters of transcriptional regulators

Author

Hélène Holota, Romain Fenouil, Frederic Koch, Jean Imbert, Muhammad Ahmad Maqbool, Salvatore Spicuglia, Marta Gut, Aurélien Griffon, Jean-Christophe Andrau, Cyrille Lepoivre, Aurélie Bergon, Laurent Vanhille, Denis Puthier, Mohamed Belhocine, Miriam Yammine, Ivo Gut, Béatrice Loriod, Joaquin Zacarias-Cabeza, Marc-Antoine Garibal, Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille - Luminy (CIML), Centre Nacional D'Anàlisi Genómica, Parc Cientific de Barcelona, ARC (project n° SFI20111203756), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), European Project: 282510,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,BLUEPRINT(2011), European Project: 262055,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-1,ESGI(2011), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Physique Théorique - UMR 7332 (CPT), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Research in SS laboratory was supported by recurrent funding from the Inserm and Aix-Marseille University, the ARC (project n° SFI20111203756) and the A*MIDEX project (n° ANR-11-IDEX-0001-02) funded by the ' Investissements d'Avenir ' French Government program., BMC, Ed., INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE - - Amidex2011 - ANR-11-IDEX-0001 - IDEX - VALID, A BLUEPRINT of Haematopoietic Epigenomes - BLUEPRINT - - EC:FP7:HEALTH2011-10-01 - 2016-09-30 - 282510 - VALID, European Sequencing and Genotyping Infrastructure - ESGI - - EC:FP7:INFRA2011-02-01 - 2015-07-31 - 262055 - VALID, Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Technologies avancées pour le génôme et la clinique ( TAGC ), Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre d'Immunologie de Marseille - Luminy ( CIML ), Centro Nacional de Análisi Genómico ( CNAG ), Centro Nacional de Análisis Genómico, ARC - project n°SFI20111203756, ANR-11-IDEX-0001-02/11-IDEX-0001,Amidex,Amidex ( 2011 ), European Project : 282510,EC:FP7:HEALTH,FP7-HEALTH-2011-single-stage,BLUEPRINT ( 2011 ), and European Project : 262055,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-1,ESGI ( 2011 )

Subjects
Transcription, Genetic, RNA polymerase II, Divergent transcription, Epigenesis, Genetic, Mice, Exon, 0302 clinical medicine, lncRNA, Transcription (biology), Transcriptional regulation, Promoter Regions, Genetic, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], Regulation of gene expression, Genetics, Base Composition, 0303 health sciences, Thymocytes, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Exons, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Chromatin, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], RNA, Long Noncoding, Research Article, Biotechnology, Biology, Developmental transcription factor, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, Epigenetics, Gene, 030304 developmental biology, GC skew, Sequence Analysis, RNA, Promoter, Mice, Inbred C57BL, Antisense Elements (Genetics), Gene Expression Regulation, Bidirectional promoter, biology.protein, CpG Islands, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery
Abstract

International audience; BACKGROUND: Divergent transcription is a wide-spread phenomenon in mammals. For instance, short bidirectional transcripts are a hallmark of active promoters, while longer transcripts can be detected antisense from active genes in conditions where the RNA degradation machinery is inhibited. Moreover, many described long non-coding RNAs (lncRNAs) are transcribed antisense from coding gene promoters. However, the general significance of divergent lncRNA/mRNA gene pair transcription is still poorly understood. Here, we used strand-specific RNA-seq with high sequencing depth to thoroughly identify antisense transcripts from coding gene promoters in primary mouse tissues. RESULTS: We found that a substantial fraction of coding-gene promoters sustain divergent transcription of long non-coding RNA (lncRNA)/mRNA gene pairs. Strikingly, upstream antisense transcription is significantly associated with genes related to transcriptional regulation and development. Their promoters share several characteristics with those of transcriptional developmental genes, including very large CpG islands, high degree of conservation and epigenetic regulation in ES cells. In-depth analysis revealed a unique GC skew profile at these promoter regions, while the associated coding genes were found to have large first exons, two genomic features that might enforce bidirectional transcription. Finally, genes associated with antisense transcription harbor specific H3K79me2 epigenetic marking and RNA polymerase II enrichment profiles linked to an intensified rate of early transcriptional elongation. CONCLUSIONS: We concluded that promoters of a class of transcription regulators are characterized by a specialized transcriptional control mechanism, which is directly coupled to relaxed bidirectional transcription.

Published
2013
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23. Identifying common and specific microRNAs expressed in peripheral blood mononuclear cell of type 1, type 2, and gestational diabetes mellitus patients

Author

Collares, C. V., Evangelista, A. F., Xavier, D. J., Rassi, D. M., Arns, T., Foss-Freitas, M. C., Foss, M. C., Puthier, Denis, Sakamoto-Hojo, E. T., Passos, G. A., Donadi, E. A., Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Spinelli, Lionel

Subjects
body regions, endocrine system diseases, embryonic structures, nutritional and metabolic diseases, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

International audience; Regardless the regulatory function of microRNAs (miRNA), their differential expression pattern has been used to define miRNA signatures and to disclose disease biomarkers. To address the question of whether patients presenting the different types of diabetes mellitus could be distinguished on the basis of their miRNA and mRNA expression profiling, we obtained peripheral blood mononuclear cell (PBMC) RNAs from 7 type 1 (T1D), 7 type 2 (T2D), and 6 gestational diabetes (GDM) patients, which were hybridized to Agilent miRNA and mRNA microarrays. Data quantification and quality control were obtained using the Feature Extraction software, and data distribution was normalized using quantile function implemented in the Aroma light package. Differentially expressed miRNAs/mRNAs were identified using Rank products, comparing T1DxGDM, T2DxGDM and T1DxT2D. Hierarchical clustering was performed using the average linkage criterion with Pearson uncentered distance as metrics.\ The use of the same microarrays platform permitted the identification of sets of shared or specific miRNAs/mRNA interaction for each type of diabetes. Nine miRNAs (hsa-miR-126, hsa-miR-1307, hsa-miR-142-3p, hsa-miR-142-5p, hsa-miR-144, hsa-miR-199a-5p, hsa-miR-27a, hsa-miR-29b, and hsa-miR-342-3p) were shared among T1D, T2D and GDM, and additional specific miRNAs were identified for T1D (20 miRNAs), T2D (14) and GDM (19) patients. ROC curves allowed the identification of specific and relevant (greater AUC values) miRNAs for each type of diabetes, including: i) hsa-miR-1274a, hsa-miR-1274b and hsa-let-7f for T1D; ii) hsa-miR-222, hsa-miR-30e and hsa-miR-140-3p for T2D, and iii) hsa-miR-181a and hsa-miR-1268 for GDM. Many of these miRNAs targeted mRNAs associated with diabetes pathogenesis.\ These results indicate that PBMC can be used as reporter cells to characterize the miRNA expression profiling disclosed by the different diabetes mellitus manifestations. Shared miRNAs may characterize diabetes as a metabolic and inflammatory disorder, whereas specific miRNAs may represent biological markers for each type of diabetes, deserving further attention.

Published
2013

24. An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function

Author

Muhammad Ahmad Maqbool, Salvatore Spicuglia, Denis Puthier, Jean-Christophe Andrau, Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), and Aix Marseille Université (AMU)

Subjects
RNA, Untranslated, RNA polymerase II, RNA-Seq, Computational biology, Genome, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Transcription (biology), Animals, Molecular Biology, 030304 developmental biology, Genetics, 0303 health sciences, Base Sequence, biology, Sequence Analysis, RNA, Gene Expression Profiling, Genetic Variation, High-Throughput Nucleotide Sequencing, RNA, Non-coding RNA, biology.protein, RNA, Long Noncoding, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 030217 neurology & neurosurgery
Abstract

International audience; The explosion of high throughput sequencing technologies marked a turn in our way of understanding the complexity and diversity of the transcriptome, including noncoding transcription dependent on RNA polymerase II. Many new ncRNA populations were described in recent years, including for example TSS RNAs, lincRNAs, eRNAs, PROMPTS and several others. Besides the advances in the average depth coverage of RNA-seq experiments, various additional protocols are now available that can be used to address qualitative and quantitative aspects of the noncoding transcriptome complexity and function. In this review, we will focus on methods allowing isolation and characterization of complex RNA populations using sequencing based approaches, including conventional strategies already used for coding genome and more specific developments allowing, for example, the study of nascent strand transcription, protein-bound or structured RNAs.

Published
2013
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25. Energy dissipation effects on imaging of soft materials by dynamic atomic force microscopy: A DNA-chip study

Author

Magali Phaner-Goutorbe, Maksym Iazykov, Yves Robach, R. Villey, Delphine Sicard, INL - Chimie et Nanobiotechnologies (INL - C&N), Institut des Nanotechnologies de Lyon (INL), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École supérieure de Chimie Physique Electronique de Lyon (CPE)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Laboratoire de Physique de la Matière Condensée et Nanostructures (LPMCN), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Institut Lumière Matière [Villeurbanne] (ILM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), INL - Hétéroepitaxie et Nanostructures (INL - H&N), and Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)

Subjects
Materials science, [SDV]Life Sciences [q-bio], Phase (waves), Biocompatible Materials, Bioengineering, 02 engineering and technology, Substrate (electronics), Microscopy, Atomic Force, 01 natural sciences, Noise (electronics), Phase Transition, Viscoelasticity, [SPI.MAT]Engineering Sciences [physics]/Materials, Biomaterials, Quantum mechanics, 0103 physical sciences, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, 010306 general physics, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, Oscillation, Spectrum Analysis, Dissipation, 021001 nanoscience & nanotechnology, Mechanics of Materials, Chemical physics, Dissipative system, Thermodynamics, 0210 nano-technology, Material properties
Abstract

Using amplitude-mode AFM (AM-AFM), we have obtained valuable information during these recent years through the study of amplitude and phase shift dependence on tip–sample separation, leading to a comprehensive understanding of the interaction processes. Two imaging regimes, attractive and repulsive, have been identified and a relationship between phase and dissipative energy was established, providing information on observed material properties. Most of the previous studies have concerned model systems: either hard or soft materials. In this paper, we present the analysis of a mixed system of soft structures on a hard substrate. This is a DNA chip for biological applications consisting of oligonucleotides covalently linked by a layer of silane to a silicon substrate. A detailed study of amplitude-phase curves as a function of the tip–sample separation allowed us to define the best experimental conditions to obtain specific information: we got reliable conditions to minimize noise during topographic imaging and an understanding of the processes of energy dissipation involved in the DNA breaking for DNA arrays. By calculating the energy dissipated as a function of the amplitude of oscillation, we have demonstrated a transition from an energy dissipation process governed by localized viscoelastic interactions (due to the soft layer) to a process governed by extended irreversible deformations (due to the hard substrate).

Published
2013
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26. Évaluation d’une méthode d’ordonnancement multicritère utilisant AHP

Author

Ounnar, Fouzia, Khader, Selma-Afakh, Dubromelle, Yves, Prunaret, Jean-Pierre, Pujo, Patrick, Laboratoire des Sciences de l'Information et des Systèmes (LSIS), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Centre National de la Recherche Scientifique (CNRS), Décision et Information pour les Systèmes de Production (DISP), Université Lumière - Lyon 2 (UL2)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Eigsi, Pujo, Patrick, and Centre National de la Recherche Scientifique (CNRS)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Université de Toulon (UTLN)-Aix Marseille Université (AMU)

Subjects
[INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, [INFO.INFO-RB] Computer Science [cs]/Robotics [cs.RO], [INFO.INFO-RB]Computer Science [cs]/Robotics [cs.RO], [INFO.INFO-AU] Computer Science [cs]/Automatic Control Engineering, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; no abstract

Published
2013

27. An introduction to photocatalysis through methylene blue photodegradation

Author

Lisa Michez, Tuhiti Malinowski, Jean-Manuel Raimundo, Philippe Dumas, Matthieu Petit, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)

Subjects
redox reaction, 82.45.Jn, 82.50.-m, 82.65.+r, 77.84.Cg, Langmuir-Hinshelwood, General Physics and Astronomy, Nanotechnology, 02 engineering and technology, 010402 general chemistry, dyes, 01 natural sciences, chemistry.chemical_compound, 11. Sustainability, TiO2, Photocatalytic degradation, Photodegradation, degradation, methylene, Physics, Reactions on surfaces, blue, Fouling, titanium dioxide, [SDE.IE]Environmental Sciences/Environmental Engineering, [CHIM.ORGA]Chemical Sciences/Organic chemistry, [CHIM.MATE]Chemical Sciences/Material chemistry, [CHIM.CATA]Chemical Sciences/Catalysis, 021001 nanoscience & nanotechnology, [SDE.ES]Environmental Sciences/Environmental and Society, 0104 chemical sciences, chemistry, Titanium dioxide, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Photocatalysis, 0210 nano-technology, photocatalysis, Methylene blue
Abstract

International audience; We described a simple experimental setup for a lab work on the photocatalytic degradation of methylene blue by T iO 2 nanoparticles. The photocatalysis process can be used for many applications. Treatments for diluted wastewaters industries, air purifying in underground car parks, preventing fouling on glass surfaces, these are some of the things this phenomenon has the ability to do. The described experiment is easy to perform and the interpretation can be easily adapted to different level of students: from high school students demonstrating their interests on a sustainable development, to students who are getting Masters in the science department that want to propose a full explanation of all the phenomenon of the photocatalytic process. Starting by a description of the experimental setup , we analysed the photocatalyst nanoparticles and applied the Langmuir-Hinshelwood model to our experimental data. Finally we discussed shortly on the respective energetic levels of the photocatalyst semiconductor and the methylene blue.

Published
2016
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28. AN AFM INVESTIGATION OF SURFACE ENERGY OF PENTACENE FILMS ON PARYLENE-C AND BENZOCYCLOBUTENE

Author

R. Villey, V. A. Skryshevsky, Maksym Iazykov, M. Erouel, Magali Phaner-Goutorbe, Eliane Souteyrand, J. Tardy, Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), INL - Chimie et Nanobiotechnologies (INL - C&N), Institut des Nanotechnologies de Lyon (INL), École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École supérieure de Chimie Physique Electronique de Lyon (CPE)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'électronique, optoélectronique et microsystèmes (LEOM), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), and Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Institut National des Sciences Appliquées de Lyon (INSA Lyon)

Subjects
Materials science, Nanotechnology, 02 engineering and technology, Triclinic crystal system, 010402 general chemistry, 01 natural sciences, Pentacene, chemistry.chemical_compound, Benzocyclobutene, Phase (matter), General Materials Science, Thin film, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, ComputingMilieux_MISCELLANEOUS, [PHYS]Physics [physics], Organic field-effect transistor, business.industry, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, Surface energy, 0104 chemical sciences, chemistry, Optoelectronics, Orthorhombic crystal system, 0210 nano-technology, business
Abstract

In view to put in light morphology peculiarities of pentacene, the widely used material for organic transistors, a detailed atomic force microscopy (AFM) investigation of the pentacene growth mode in relationship with the film thickness (in the range 6–60 nm) is reported. Local surface energy measurements based on contact AFM spectroscopy were performed to explain the thickness dependent morphology of the pentacene films onto two polymer dielectrics (parylene-C and benzocyclobutene). Our analysis provided an exhaustive description not only of the accessible film surface but also of its inner structural properties. Evidenced by these approaches, a critical thickness of 30 nm was found in relation with a transition from the orthorhombic thin film phase to triclinic bulk phase for pentacene growth on parylene-C and benzocyclobutene. This thickness was previously observed to be corresponding to organic field effect transistors (OFETs) with optimized mobility.

Published
2012
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29. Isoarchic control for intelligent entities in manufacturing

Author

Ounnar, Fouzia, Pujo, Patrick, Dubromelle, Yves, Louati, Thamer, Prunaret, Jean-Pierre, Laboratoire des Sciences de l'Information et des Systèmes (LSIS), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Centre National de la Recherche Scientifique (CNRS), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Duncan Mc Farlane, Centre National de la Recherche Scientifique (CNRS)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Université de Toulon (UTLN)-Aix Marseille Université (AMU), and Pujo, Patrick

Subjects
[INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, [INFO.INFO-RB] Computer Science [cs]/Robotics [cs.RO], [INFO.INFO-RB]Computer Science [cs]/Robotics [cs.RO], [INFO.INFO-AU] Computer Science [cs]/Automatic Control Engineering, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; no abstract

Published
2012

30. Service Oriented Architecture in PROSIS holonic control

Author

Dubromelle, Yves, Ounnar, Fouzia, Prunaret, Jean-Pierre, Pujo, Patrick, Laboratoire des Sciences de l'Information et des Systèmes (LSIS), Centre National de la Recherche Scientifique (CNRS)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Université de Toulon (UTLN)-Aix Marseille Université (AMU), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Centre National de la Recherche Scientifique (CNRS), and Pujo, Patrick

Subjects
Isoarchic architecture, Holonic control, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, [INFO.INFO-RB] Computer Science [cs]/Robotics [cs.RO], SOA, [INFO.INFO-RB]Computer Science [cs]/Robotics [cs.RO], PROSIS model, Ambient services, [INFO.INFO-AU] Computer Science [cs]/Automatic Control Engineering
Abstract

May 25 - May 27; International audience; Ambient intelligence applied to manufacturing systems will deeply transform approaches to production organization and control. Infotronics technologies will enlarge the capabilities to interact, to react and to customize control systems with innovative possibilities that should already be envisaged and thoroughly studied. Indeed, beyond identification, traceability and security applications that are generally considered, these technologies offer the possibility to associate to each entity, constituting a production system, a decisional intelligence. Autonomy properties are thus associated to the entity. Under these new advances, a control system based on the holonic paradigm and an isoarchic architecture, named PROSIS (Product, Resource, Order, Simulation Isoarchical System), was proposed. This approach provides a range of ambient services to the holonic entities. The aim of this paper is to present the service oriented architecture in the PROSIS control system. After presenting the holonic control system (PROSIS) model, the ambient services that can be provided are described and the way these services could be delivered are presented.

Published
2011

31. Simulation du transport de particules dans la structure poreuse d’une membrane de filtration

Author

Derekx, Quentin, Veyret, Damien, Glucina, Karl, Bacchin, Patrice, Moulin, Philippe, Service irevues, irevues, Association Française de Mécanique, Laboratoire de Génie Chimique (LGC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), SUEZ ENVIRONNEMENT (FRANCE), Laboratoire de Mécanique, Modélisation et Procédés Propres (M2P2), and Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.MECA]Physics [physics]/Mechanics [physics], [PHYS.MECA] Physics [physics]/Mechanics [physics]
Abstract

Colloque avec actes et comité de lecture. Internationale.; International audience; Actuellement, la description des procédés membranaires est principalement macroscopique, et ainsi, manque de précision. De ce fait, la connaissance de l’écoulement au niveau des pores est de première importance. Toutefois, cette échelle microscopique est difficilement accessible par voie expérimentale et par simulation numérique. Dans cette étude, des milieux poreux tridimensionnels complexes sont générés de façon aléatoire ou bien à partir de visualisations expérimentales obtenues par tomographie par exemple, puis les écoulements sont calculés en prenant en compte la capture des particules par effet stérique ou par adhésion...

Published
2009

32. Chapter 7. Agent-based Simulation of Business Network Planning andCoordination Systems

Author

Monteiro, Thibaud, Anciaux, Didier, d'Amours, Sophie, Espinasse, Bernard, Ferrarini, Alain, Labarthe, Olivier, Montreuil, B., Roy, Daniel, Laboratoire de Génie Industriel et de Production de Metz (LGIPM), Université Paul Verlaine - Metz (UPVM), Optimal and secure management of manufacturing systems (COSTEAM), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Paul Verlaine - Metz (UPVM), Consortium de recherche for@c (FORAC), CIRRELT, Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Laboratoire des Sciences de l'Information et des Systèmes (LSIS), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Centre National de la Recherche Scientifique (CNRS), Laboratoire CIRRELT Université Laval Quebec (CIRRELT), Université Laval [Québec] (ULaval), Caroline Thierry and Andre Thomas and Gerard Bel, and Centre National de la Recherche Scientifique (CNRS)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Université de Toulon (UTLN)-Aix Marseille Université (AMU)

Subjects
[INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2008

33. Chapitre 6. L'intérêt des agents pour la simulation de la chaîne logistique

Author

Monteiro, Thibaud, Anciaux, Didier, Espinasse, Bernard, Ferrarini, Alain, Labarthe, Olivier, Montreuil, B., Roy, Daniel, Laboratoire de Génie Industriel et de Production Mécanique (LGIPM), Université Paul Verlaine - Metz (UPVM), Optimal and secure management of manufacturing systems (COSTEAM), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Paul Verlaine - Metz (UPVM), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Laboratoire des Sciences de l'Information et des Systèmes (LSIS), Centre National de la Recherche Scientifique (CNRS)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Université de Toulon (UTLN)-Aix Marseille Université (AMU), Laboratoire CIRRELT Université Laval Quebec (CIRRELT), Université Laval [Québec] (ULaval), Caroline Thierry and Andre Thomas and Gerard Bel, and Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Centre National de la Recherche Scientifique (CNRS)

Subjects
[INFO.INFO-PF]Computer Science [cs]/Performance [cs.PF], [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2008

34. Chapitre 7. Simulation à base d'agents des systèmes de coordination et de planification des réseaux d'entreprise

Author

Monteiro, Thibaud, Anciaux, Didier, D'Amours, Sophie, Espinasse, Bernard, Ferrarini, Alain, Labarthe, Olivier, Montreuil, B., Roy, Daniel, Optimal and secure management of manufacturing systems (COSTEAM), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Paul Verlaine - Metz (UPVM), Laboratoire de Génie Industriel et de Production Mécanique (LGIPM), Université Paul Verlaine - Metz (UPVM), Consortium de recherche for@c (FORAC), CIRRELT, Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Laboratoire des Sciences de l'Information et des Systèmes (LSIS), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Centre National de la Recherche Scientifique (CNRS), Laboratoire CIRRELT Université Laval Quebec (CIRRELT), Université Laval [Québec] (ULaval), Caroline Thierry and Andre Thomas and Gerard Bel, and Centre National de la Recherche Scientifique (CNRS)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Université de Toulon (UTLN)-Aix Marseille Université (AMU)

Subjects
[INFO.INFO-PF]Computer Science [cs]/Performance [cs.PF], [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2008

35. Chapter 6. The Interest of Agents for Supply Chain Simulation

Author

Monteiro, Thibaud, Anciaux, Didier, Espinasse, Bernard, Ferrarini, Alain, Labarthe, Olivier, Montreuil, B., Roy, Daniel, Optimal and secure management of manufacturing systems (COSTEAM), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Paul Verlaine - Metz (UPVM), Laboratoire de Génie Industriel et de Production Mécanique (LGIPM), Université Paul Verlaine - Metz (UPVM), Polytech Marseille (AMU POLYTECH), Aix Marseille Université (AMU), Laboratoire des Sciences de l'Information et des Systèmes (LSIS), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Centre National de la Recherche Scientifique (CNRS), Laboratoire CIRRELT Université Laval Quebec (CIRRELT), Université Laval [Québec] (ULaval), Caroline Thierry and Andre Thomas and Gerard Bel, and Centre National de la Recherche Scientifique (CNRS)-Arts et Métiers Paristech ENSAM Aix-en-Provence-Université de Toulon (UTLN)-Aix Marseille Université (AMU)

Subjects
[INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2008

36. P3 : un outil pour la formation à la gestion et au pilotage d'ateliers de production

Author

Patrick Pujo, Ounnar, F., Borriello, B., sylvie contreras, Gonzalez, M. C., Pujo, Patrick, Polytech Marseille (AMU POLYTECH), and Aix Marseille Université (AMU)

Subjects
[INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, [INFO.INFO-RB] Computer Science [cs]/Robotics [cs.RO], [INFO.INFO-RB]Computer Science [cs]/Robotics [cs.RO], [INFO.INFO-AU] Computer Science [cs]/Automatic Control Engineering, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; no abstract

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