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5,107 results on '"King Abdullah University of Science and Technology (KAUST)"'

1. Substrate-Induced Phase in a discotic liquid crystal

Author: International Colloquium on Flexible Electronics and Photovoltaics (ICFE-PV) (November 2-5, 2013: King Abdullah University of Science and Technology (KAUST), Saudi Arabia), Chattopadhyay, Basab, Geerts, Yves, International Colloquium on Flexible Electronics and Photovoltaics (ICFE-PV) (November 2-5, 2013: King Abdullah University of Science and Technology (KAUST), Saudi Arabia), Chattopadhyay, Basab, and Geerts, Yves
Abstract: info:eu-repo/semantics/nonPublished
Published: 2013

2. In vitro anti-atherogenic properties of N-heterocyclic carbene aurate(I) compounds

Author: King Abdullah University of Science and Technology(KAUST), Sioriki, Eleni, Lordan, Ronan, Nahra, Fady, Van Hecke, Kristof, Zabetakis, Ioannis, Nolan, Steven P., King Abdullah University of Science and Technology(KAUST), Sioriki, Eleni, Lordan, Ronan, Nahra, Fady, Van Hecke, Kristof, Zabetakis, Ioannis, and Nolan, Steven P.
Abstract: peer-reviewed, The anti‐atherogenic (anti‐inflammatory) properties of various aurate(I) salts, of the general formula [NHC⋅H][AuCl2] (NHC=N‐heterocyclic carbene) were investigated. The aurates were easily synthesized and obtained in analytically pure form. In addition, the biological activity of these compounds against atheromatosis via in vitro inhibition of platelet‐activating factor (PAF)‐induced platelet aggregation was probed. All complexes were found to possess anti‐aggregatory properties in vitro with [IPr*⋅H][AuCl2] (6) being the most potent inhibitor of PAF at micromolar concentration. Based on our findings, we conclude that these simply assembled aurates are a very promising class of PAF inhibitors and anti‐inflammatory drugs.

3. Emergence of Coherent Localized Structures in Shear Deformations of Temperature Dependent Fluids

Author: institute of applied and computational mathematics ; Foundation for Research & Technology - Hellas, Department of Applied Mathematics ; University of Crete, Aix-Marseille Université (AMU), King Abdullah University of Science and Technology (KAUST) ; King Abdullah University of Science and Technology, Aristeia program of the Greek Secretariat of Research, European Project : 245749, REGPOT, FP7-REGPOT-2009-1, ACMAC(2010), Katsaounis, Theodoros, Olivier, Julier, Tzavaras, Athanasios, institute of applied and computational mathematics ; Foundation for Research & Technology - Hellas, Department of Applied Mathematics ; University of Crete, Aix-Marseille Université (AMU), King Abdullah University of Science and Technology (KAUST) ; King Abdullah University of Science and Technology, Aristeia program of the Greek Secretariat of Research, European Project : 245749, REGPOT, FP7-REGPOT-2009-1, ACMAC(2010), Katsaounis, Theodoros, Olivier, Julier, and Tzavaras, Athanasios
Abstract: Shear localization occurs in various instances of material instability in solid mechanics and is typically associated with Hadamard-instability for an underlying model. While Hadamard instability indicates the catastrophic growth of oscillations around a mean state, it does not by itself explain the formation of coherent structures typically observed in localization. The latter is a nonlinear effect and its analysis is the main objective of this article. We consider a model that captures the main mechanisms observed in high strain-rate deformation of metals, and describes shear motions of temperature dependent non-Newtonian fluids. For a special dependence of the viscosity on the temperature, we carry out a linearized stability analysis around a base state of uniform shearing solutions, and quantitatively assess the effects of the various mechanisms affecting the problem: thermal softening, momentum diffusion and thermal diffusion. Then, we turn to the nonlinear model, and construct localized states -in the form of similarity solutions -that emerge as coherent structures in the localization process. This justifies a scenario for localization that is proposed on the basis of asymptotic analysis in [10].

4. Essential role of the CD docking motif of MPK4 in plant immunity, growth, and development

Author: Anna Siodmak, Umar F. Shahul Hameed, Naganand Rayapuram, Ronny Völz, Marie Boudsocq, Siba Alharbi, Hannah Alhoraibi, Yong‐Hwan Lee, Ikram Blilou, Stefan T. Arold, Heribert Hirt, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center, Research Institute of Agriculture and Life Sciences [Seoul], Seoul National University [Seoul] (SNU), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, Plant Immunity Research Center, Centre de Biologie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Max Perutz Laboratories, University of Vienna [Vienna], King Abdullah University of Science and Technology (KAUST) to HH (BAS/1/1062-01-01) and STA (BAS/1/1056-01-01), and Award no. URF/1/2965-01 from the Ofﬁce of Sponsored Research (OSR)
Subjects: reactive oxygen species, MPK4, Physiology, oxidation, Plant Science, kinase activity, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, immunity, [SDV.BDD]Life Sciences [q-bio]/Development Biology, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity
Abstract: International audience; MAPKs are universal eukaryotic signaling factors whose functioning is assumed to depend on the recognition of a common docking motif (CD) by its activators, substrates, and inactiva- tors. We studied the role of the CD domain of Arabidopsis MPK4 by performing interaction stu- dies and determining the ligand-bound MPK4 crystal structure. We revealed that the CD domain of MPK4 is essential for interaction and activation by its upstream MAPKKs MKK1, MKK2, and MKK6. Cys181 in the CD site of MPK4 was shown to become sulfenylated in response to reactive oxygen species in vitro. To test the function of C181 in vivo, we generated wild-type (WT) MPK4-C181, nonsulfenylatable MPK4-C181S, and potentially sulfenylation mimicking MPK4-C181D lines in the mpk4 knockout back- ground. We analyzed the phenotypes in growth, development, and stress responses, reveal- ing that MPK4-C181S has WT activity and complements the mpk4 phenotype. By contrast, MPK4-C181D cannot be activated by upstream MAPKK and cannot complement the pheno- types of mpk4. Our ﬁndings show that the CD motif is essential and is required for activation by upstream MAPKK for MPK4 function. Furthermore, growth, development, or immunity functions require upstream activation of the MPK4 protein kinase.
Published: 2023

5. Performance analysis of economic model predictive control on a solar-powered direct contact membrane distillation system

Author: Hichem Bessafa, Ghania Khodja, Chakir Messaoud, Taous-Meriem Laleg-Kirati, King Abdullah University of Science and Technology [KAUST], Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL], King Abdullah University of Science and Technology (KAUST), Ecole Polytechnique of Algiers (ENP), Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université de Lille, and Estimation Modelling and ANalysis Group (KAUST-CEMSE)
Subjects: Control and Systems Engineering, [MATH.MATH-MP]Mathematics [math]/Mathematical Physics [math-ph]
Abstract: International audience
Published: 2022

6. Multiscale Unfolding: Illustratively Visualizing the Whole Genome at a Glance

Author: Halladjian, Sarkis, Kouřil, David, Miao, Haichao, Gröller, Eduard, Viola, Ivan, Isenberg, Tobias, Analysis and Visualization (AVIZ), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Interaction avec l'Humain (IaH), Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institute of Visual Computing & Human-Centered Technology, Vienna University of Technology (TU Wien), Institute of Computer Graphics and Algorithms, Visual Computing Center, King Abdullah University of Science and Technology, Part of this work was funded under the ILLUSTRARE grant by both the Austrian Science Fund (FWF): I 2953-N31 and the French National Research Agency (ANR): ANR-16-CE91-0011-01. The research was further supported by funding from King Abdullah University of Science and Technology (KAUST), under award number BAS/1/1680-01-01 and by funding from the ILLVISATION grant by WWTF (VRG11-010)., ANR-16-CE91-0011,ILLUSTRARE,Integrative Visual Abstraction of Molecular Data(2016), Analysis and Visualization (AViz), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Interaction avec l'Humain (IaH), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec, Technical University of Vienna [Vienna] (TU WIEN), King Abdullah University of Science and Technology (KAUST), Part of this work was funded under the ILLUSTRARE grant by both the Austrian Science Fund (FWF): I 2953-N31 and the French National Research Agency (ANR): ANR-16-CE91-0011-01. The research was further supported by funding from King Abdullah University of Science and Technology(KAUST), under award number BAS/1/1680-01-01 and by funding from the ILLVISATION grant by WWTF (VRG11-010)., Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Interaction avec l'Humain (IaH), and Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: Multiscale visualization, visual abstraction, [SCCO.COMP]Cognitive science/Computer science, spatially-controlled scale transition, DNA, illustrative visualization, genome
Abstract: International audience; We present Multiscale Unfolding, an interactive technique for illustratively visualizing multiple hierarchical scales of DNA in a single view, showing the genome at different scales and demonstrating how one scale spatially folds into the next. The DNA's extremely long sequential structure---arranged differently on several distinct scale levels---is often lost in traditional 3D depictions, mainly due to its multiple levels of dense spatial packing and the resulting occlusion. Furthermore, interactive exploration of this complex structure is cumbersome, requiring visibility management like cutaways. In contrast to existing temporally controlled multiscale data exploration, we allow viewers to always see and interact with any of the involved scales. For this purpose we separate the depiction into constant-scale and scale transition zones. Constant-scale zones maintain a single-scale representation, while still linearly unfolding the DNA. Inspired by illustration, scale transition zones connect adjacent constant-scale zones via level unfolding, scaling, and transparency. We thus represent the spatial structure of the whole DNA macro-molecule, maintain its local organizational characteristics, linearize its higher-level organization, and use spatially controlled, understandable interpolation between neighboring scales. We also contribute interaction techniques that provide viewers with a coarse-to-fine control for navigating within our all-scales-in-one-view representations and visual aids to illustrate the size differences. Overall, Multiscale Unfolding allows viewers to grasp the DNA's structural composition from chromosomes to the atoms, with increasing levels of "unfoldedness," and can be applied in data-driven illustration and communication.
Published: 2022

7. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

Author: Xiaoqin Zou, Théo Mauri, Hang Shi, Shaowen Zhu, Justas Dapkūnas, Yuanfei Sun, Didier Barradas-Bautista, Raphael A. G. Chaleil, Ragul Gowthaman, Sohee Kwon, Xianjin Xu, Zuzana Jandova, Genki Terashi, Ryota Ashizawa, Petras J. Kundrotas, Shuang Zhang, Tunde Aderinwale, Jian Liu, Sandor Vajda, Paul A. Bates, Jianlin Cheng, Daisuke Kihara, Luis A. Rodríguez-Lumbreras, Carlos A. Del Carpio Muñoz, Liming Qiu, Guillaume Brysbaert, Jorge Roel-Touris, Česlovas Venclovas, Tereza Clarence, Rui Yin, Amar Singh, Patryk A. Wesołowski, Rafał Ślusarz, Adam Liwo, Guangbo Yang, Agnieszka S. Karczyńska, Yoshiki Harada, Sergei Kotelnikov, Yuya Hanazono, Charlotte W. van Noort, Marc F. Lensink, Jonghun Won, Adam K. Sieradzan, Israel Desta, Xufeng Lu, Charles Christoffer, Anna Antoniak, Taeyong Park, Sheng-You Huang, Tsukasa Nakamura, Brian G. Pierce, Usman Ghani, Yang Shen, Luigi Cavallo, Chaok Seok, Hao Li, Nurul Nadzirin, Ghazaleh Taherzadeh, Jacob Verburgt, Rodrigo V. Honorato, Artur Giełdoń, Jeffrey J. Gray, Dima Kozakov, Ming Liu, Shan Chang, Eiichiro Ichiishi, Manon Réau, Rui Duan, Francesco Ambrosetti, Johnathan D. Guest, Juan Fernández-Recio, Alexandre M. J. J. Bonvin, Ilya A. Vakser, Farhan Quadir, Yumeng Yan, Ren Kong, Sameer Velankar, Sergei Grudinin, Mateusz Kogut, Mikhail Ignatov, Yasuomi Kiyota, Hyeonuk Woo, Shoshana J. Wodak, Ameya Harmalkar, Shinpei Kobayashi, Panagiotis I. Koukos, Zhen Cao, Kliment Olechnovič, Cezary Czaplewski, Xiao Wang, Agnieszka G. Lipska, Kathryn A. Porter, Peicong Lin, Emilia A. Lubecka, Nasser Hashemi, Bin Liu, Mayuko Takeda-Shitaka, Karolina Zięba, Dzmitry Padhorny, Zhuyezi Sun, Daipayan Sarkar, Romina Oliva, Andrey Alekseenko, Siri Camee van Keulen, Mireia Rosell, Raj S. Roy, Brian Jiménez-García, Jinsol Yang, Martyna Maszota-Zieleniak, Cancer Research UK, Department of Energy and Climate Change (UK), European Commission, Institut National de Recherche en Informatique et en Automatique (France), Medical Research Council (UK), Japan Society for the Promotion of Science, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), National Institute of General Medical Sciences (US), National Institutes of Health (US), National Natural Science Foundation of China, National Science Foundation (US), Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Biomolecular Modelling Laboratory [London], The Francis Crick Institute [London], Jiangsu University of Technology [Changzhou], Department of Electrical Engineering and Computer Science [Columbia] (EECS), University of Missouri [Columbia] (Mizzou), University of Missouri System-University of Missouri System, Institute for Data Science and Informatics [Columbia], University of Gdańsk (UG), Faculty of Electronics, Telecommunications and Informatics [GUT Gdańsk] (ETI), Gdańsk University of Technology (GUT), Medical University of Gdańsk, Graduate School of Medical Sciences [Nagoya], Nagoya City University [Nagoya, Japan], International University of Health and Welfare Hospital (IUHW Hospital), Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University (JHU), Bijvoet Center of Biomolecular Research [Utrecht], Utrecht University [Utrecht], Stony Brook University [SUNY] (SBU), State University of New York (SUNY), Innopolis University, Boston University [Boston] (BU), Russian Academy of Sciences [Moscow] (RAS), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Universidad de La Rioja (UR), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Données, Apprentissage et Optimisation (DAO), Laboratoire Jean Kuntzmann (LJK), Université Grenoble Alpes (UGA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Huazhong University of Science and Technology [Wuhan] (HUST), Indiana University - Purdue University Indianapolis (IUPUI), Indiana University System, Graduate School of Information Sciences [Sendaï], Tohoku University [Sendai], National Institutes for Quantum and Radiological Science and Technology (QST), University of Maryland [Baltimore], King Abdullah University of Science and Technology (KAUST), University of Naples Federico II, Texas A&M University [Galveston], Seoul National University [Seoul] (SNU), Kitasato University, University of Kansas [Lawrence] (KU), Vilnius University [Vilnius], University of Missouri System, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Sub NMR Spectroscopy, Sub Overig UiLOTS, Sub Mathematics Education, NMR Spectroscopy, Université de Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576, European Bioinformatics Institute [Hinxton] [EMBL-EBI], Department of Electrical Engineering and Computer Science [Columbia] [EECS], Faculty of Chemistry [Univ Gdańsk], Faculty of Electronics, Telecommunications and Informatics [GUT Gdańsk] [ETI], International University of Health and Welfare Hospital [IUHW Hospital], Johns Hopkins University [JHU], Stony Brook University [SUNY] [SBU], Department of Biomedical Engineering [Boston], Instituto de Ciencias de la Vid y el Vino [ICVV], Huazhong University of Science and Technology [Wuhan] [HUST], Indiana University - Purdue University Indianapolis [IUPUI], National Institutes for Quantum and Radiological Science and Technology [QST], King Abdullah University of Science and Technology [KAUST], Università degli Studi di Napoli 'Parthenope' = University of Naples [PARTHENOPE], Seoul National University [Seoul] [SNU], University of Kansas [Lawrence] [KU], University of Missouri [Columbia] [Mizzou], Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), University of Naples Federico II = Università degli studi di Napoli Federico II, European Project: 675728,H2020,H2020-EINFRA-2015-1,BioExcel(2015), European Project: 823830,H2020-EU.1.4.1.3. Development, deployment and operation of ICT-based e-infrastructures, H2020-EU.1.4. EXCELLENT SCIENCE - Research Infrastructures ,BioExcel-2(2019), European Project: 777536,H2020-EU.1.4.1.3. Development, deployment and operation of ICT-based e-infrastructures, and H2020-EU.1.4. EXCELLENT SCIENCE - Research Infrastructures,EOSC-hub(2018)
Subjects: Models, Molecular, blind prediction, CAPRI, CASP, docking, oligomeric state, protein assemblies, protein complexes, protein docking, protein–protein interaction, template-based modeling, Computer science, [SDV]Life Sciences [q-bio], Machine learning, computer.software_genre, Biochemistry, Article, protein-protein interaction, 03 medical and health sciences, Sequence Analysis, Protein, Structural Biology, Server, Protein Interaction Domains and Motifs, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Binding Sites, business.industry, 030302 biochemistry & molecular biology, Computational Biology, Proteins, 3. Good health, Molecular Docking Simulation, Artificial intelligence, business, computer, Software
Abstract: We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands., Cancer Research UK, Grant/Award Number: FC001003; Changzhou Science and Technology Bureau, Grant/Award Number: CE20200503; Department of Energy and Climate Change, Grant/Award Numbers: DE-AR001213, DE-SC0020400, DE-SC0021303; H2020 European Institute of Innovation and Technology, Grant/Award Numbers: 675728, 777536, 823830; Institut national de recherche en informatique et en automatique (INRIA), Grant/Award Number: Cordi-S; Lietuvos Mokslo Taryba, Grant/Award Numbers: S-MIP-17-60, S-MIP-21-35; Medical Research Council, Grant/Award Number: FC001003; Japan Society for the Promotion of Science KAKENHI, Grant/Award Number: JP19J00950; Ministerio de Ciencia e Innovación, Grant/Award Number: PID2019-110167RB-I00; Narodowe Centrum Nauki, Grant/Award Numbers: UMO-2017/25/B/ST4/01026, UMO-2017/26/M/ST4/00044, UMO-2017/27/B/ST4/00926; National Institute of General Medical Sciences, Grant/Award Numbers: R21GM127952, R35GM118078, RM1135136, T32GM132024; National Institutes of Health, Grant/Award Numbers: R01GM074255, R01GM078221, R01GM093123, R01GM109980, R01GM133840, R01GN123055, R01HL142301, R35GM124952, R35GM136409; National Natural Science Foundation of China, Grant/Award Number: 81603152; National Science Foundation, Grant/Award Numbers: AF1645512, CCF1943008, CMMI1825941, DBI1759277, DBI1759934, DBI1917263, DBI20036350, IIS1763246, MCB1925643; NWO, Grant/Award Number: TOP-PUNT 718.015.001; Wellcome Trust, Grant/Award Number: FC001003
Published: 2021

8. Experimental and Numerical Investigation of the Response of a Swirled Flame to Flow Modulations in a Non-Adiabatic Combustor

Author: Adrien Chatelier, Thierry Schuller, Thibault F. Guiberti, Renaud Mercier, Benoit Fiorina, Nicolas Bertier, Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), King Abdullah University of Science and Technology - KAUST (SAUDI ARABIA), Office National d'Etudes et Recherches Aérospatiales - ONERA (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), SAFRAN (FRANCE), Institut de Mécanique des Fluides de Toulouse - IMFT (Toulouse, France), Laboratoire d'Énergétique Moléculaire et Macroscopique, Combustion (EM2C), Université Paris Saclay (COmUE)-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec, DMPE, ONERA, Université Paris Saclay (COmUE) [Châtillon], ONERA-Université Paris Saclay (COmUE), King Abdullah University of Science and Technology (KAUST), SAFRAN Group, Institut de mécanique des fluides de Toulouse (IMFT), 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, and Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE)
Subjects: Work (thermodynamics), Swirling flames, Computer science, Mécanique des fluides, 020209 energy, General Chemical Engineering, Flame transfer function, General Physics and Astronomy, 02 engineering and technology, 01 natural sciences, 010305 fluids & plasmas, Turbulent premixed combustion, 0103 physical sciences, 0202 electrical engineering, electronic engineering, information engineering, [PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Fluid mechanics [physics.class-ph], Non-adiabatic combustion, Physical and Theoretical Chemistry, Aerospace engineering, Adiabatic process, business.industry, Flame dynamics, Flow (mathematics), Combustor, Christian ministry, business, Flow solver
Abstract: International audience; Turbulent combustion models for Large Eddy Simulation (LES) aims at predicting the flame dynamics. So far, they have been proven to predict correctly the mean flow and flame properties in a wide range of configurations. A way to challenge these models in unsteady situations is to test their ability to recover turbulent flames submitted to harmonic flow modulations. In this study, the Flame Transfer Function (FTF) of a CH4/H2/air premixed swirled-stabilized flame submitted to harmonic flowrate modulations in a non-adiabatic combustor is compared to the response computed using the Filtered TAbulated Chemistry for LES (F-TACLES) formalism. Phase averaged analysis of the perturbed flow field and flame response reveal that the velocity field determined with Particle Image Velocimetry measurements, the heat release distribution inferred from OH* images and the probability of presence of burnt gases deduced from OH-Planar Laser Induced Fluorescence measure- ments are qualitatively well reproduced by the simulations. However, noticeable differences between experiments and simulations are also observed in a narrow frequency range. A detailed close-up view of the flow field highlight differences in experimental OH* and numerical volumetric heat release rate distributions which are at the origin of the differences observed between the numerical and experimental FTF. These differences mainly originate from the outer shear layer of the swirling jet where a residual reaction layer takes place in the simulations which is absent in the experiments. Consequences for turbulent combustion modeling are suggested by examining the evolution of the perturbed flame brush envelope along the downstream distance of the perturbed flames. It is shown that changing the grid resolution and the flame subgrid scale wrinkling factor in these regions does not alter the numerical results. It is finally concluded that the combined effects of strain rate and enthalpy defect due to heat losses are the main factors leading to small but sizable differences of the flame response to coherent structures synchronized by the acoustic forcing in the outer shear layer of the swirling flow. These small differences in flame response lead in turn to a misprediction of the FTF at specific forcing frequencies.
Published: 2019

9. Max‐infinitely divisible models and inference for spatial extremes

Author: Raphaël Huser, Thomas Opitz, Emeric Thibaud, King Abdullah University of Science and Technology (KAUST), Biostatistique et Processus Spatiaux (BioSP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecole Polytechnique Fédérale de Lausanne (EPFL), and King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) OSR-CRG2017-3434
Subjects: Statistics and Probability, asymptotic dependence and independence, infinitely divisible process, 05 social sciences, Inference, Supercomputer, block maximum approach, 01 natural sciences, max&#8208, 010104 statistics & probability, Work (electrical), subasymptotic modeling, 0502 economics and business, [SDE]Environmental Sciences, 0101 mathematics, Statistics, Probability and Uncertainty, extreme event, Mathematical economics, wind speed, 050205 econometrics, Mathematics
Abstract: International audience; For many environmental processes, recent studies have shown that the dependence strength is decreasing when quantile levels increase. This implies that the popular max-stable models are inadequate to capture the rate of joint tail decay, and to estimate joint extremal probabilities beyond observed levels. We here develop a more flexible modeling framework based on the class of max-infinitely divisible processes, which extend max-stable processes while retaining dependence properties that are natural for maxima. We propose two parametric constructions for max-infinitely divisible models, which relax the max-stability property but remain close to some popular max-stable models obtained as special cases. The first model considers maxima over a finite, random number of independent observations, while the second model generalizes the spectral representation of max-stable processes. Inference is performed using a pairwise likelihood. We illustrate the benefits of our new modeling framework on Dutch wind gust maxima calculated over different time units. Results strongly suggest that our proposed models outperform other natural models, such as the Student-t copula process and its max-stable limit, even for large block sizes.
Published: 2021

10. Sample average approximation for risk-averse problems: A virtual power plant scheduling application

Author: Antonio J. Conejo, Omar M. Knio, Ricardo Lima, Loïc Giraldi, Ibrahim Hoteit, Olivier Le Maitre, King Abdullah University of Science and Technology (KAUST), Ohio State University [Columbus] (OSU), Technocentre Renault [Guyancourt], RENAULT, Uncertainty Quantification in Scientific Computing and Engineering (PLATON), Centre de Mathématiques Appliquées - Ecole Polytechnique (CMAP), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), and Research reported in this publication was supported by research funding from King Abdullah University of Science and Technology (KAUST). Antonio J. Conejo’s contribution is partly supported by NSF project 1808169.
Subjects: Mathematical optimization, Control and Optimization, Computer science, 020209 energy, 0211 other engineering and technologies, Scheduling (production processes), 02 engineering and technology, Management Science and Operations Research, Wind speed, Virtual power plant, 0202 electrical engineering, electronic engineering, information engineering, Sample average approximation, Risk-averse stochastic programming, T57-57.97, 021103 operations research, Applied mathematics. Quantitative methods, business.industry, Estimator, QA75.5-76.95, Stochastic programming, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], Computational Mathematics, Expected shortfall, Sample size determination, Modeling and Simulation, Electronic computers. Computer science, Electricity, [MATH.MATH-OC]Mathematics [math]/Optimization and Control [math.OC], business
Abstract: International audience; In this paper, we address the decision-making problem of a virtual power plant (VPP) involving a self-scheduling and market involvement problem under uncertainty in the wind speed and electricity prices. The problem is modeled using a risk-neutral and two risk-averse two-stage stochastic programming formulations, where the conditional value at risk is used to represent risk. A sample average approximation methodology is integrated with an adapted L-Shaped solution method, which can solve risk-neutral and specific risk-averse problems. This methodology provides a framework to understand and quantify the impact of the sample size on the variability of the results. The numerical results include an analysis of the computational performance of the methodology for two case studies, estimators for the bounds of the true optimal solutions of the problems, and an assessment of the quality of the solutions obtained. In particular, numerical experiences indicate that when an adequate sample size is used, the solution obtained is close to the optimal one.
Published: 2021

11. The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching

Author: Zelinda Maria Braga Hirano, Daniel C. Jeffares, Cristiana Ferreira Alves de Brito, Olga Douvropoulou, Alcides Pissinatti, Qingtian Guan, Cesare Bianco Júnior, Anielle de Pina-Costa, Tobias Mourier, Sarah Forrester, Abhinav Kaushik, Cláudio Tadeu Daniel-Ribeiro, Arnab Pain, Stefan T. Arold, Filipe Vieira Santos de Abreu, Júlio César de Souza Junior, Maria de Fátima Ferreira-da-Cruz, Silvia Bahadian Moreira, Patrícia Brasil, Francisco J. Guzmán-Vega, Denise Anete Madureira de Alvarenga, Ricardo Lourenço de Oliveira, Richard Culleton, Malbec, Odile, King Abdullah University of Science and Technology (KAUST), Fiocruz Minas - René Rachou Research Center / Instituto René Rachou [Belo Horizonte, Brésil], Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centro de Pesquisa, Diagnóstico e Treinamento em Malária [Rio de Janeiro] (CPD-MAL), Instituto Oswaldo Cruz / Oswaldo Cruz Institute [Rio de Janeiro] (IOC), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Fundação Oswaldo Cruz (FIOCRUZ), Instituto Nacional de Infectologia Evandro Chagas [Rio de Janeiro] (INI), Centro Universitário Serra dos Órgãos [Teresópolis, RJ, Brazil] (UNIFESO), University of York [York, UK], Laboratório de Mosquitos Transmissores de Hematozoários [Rio de Janeiro], Pesquisa em Malária [Rio de Janeiro], Universidade Regional de Blumenau (FURB), Centro de Primatologia do Rio de Janeiro [Guapimirim, Brazil] (CPRJ/Inea), Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Ehime University [Matsuyama, Japon], Hokkaido University [Sapporo, Japan], The work was supported financially by the King Abdullah University of Science and Technology (KAUST) through the baseline fund BRF1020/01/01 to AP and BAS/1/1056-01-01 to STA, and the Award No. URF/1/1976-25 from the Office of Sponsored Research (OSR). The field work in the Atlantic Forest and laboratory analysis in Brazil received financial support from the Secretary for Health Surveillance of the Ministry of Health through the Global Fund (agreement IOC-005-Fio-13), Programa Nacional de Excelência (PRONEX) and contract 407873/2018-0 of the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), the Fundação de Amparo à Pesquisa do Estado de Minas Gerais (Fapemig CBB-APQ-02620-15) and the Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (Faperj), Brazil. CNPq supports CFAB, CTDR, MFFC, PB and RLO, with a research productivity fellowship. CTDR (CNE: E-26/202.921/2018), MFFC, PB and RLO are also supported by Faperj as Cientistas do nosso estado. AdP-C was supported by a postdoctoral fellowship from the Faperj and DAMA by a fellowship from the CGZV-SVS (Brazilian Ministry of Health) TED 49/2018 grant. SF was supported by a Wellcome Seed Award in Science to DCJ (208965/Z/17/Z)., King Abdullah University of Science and Technology, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Ehime University [Matsuyama]
Subjects: Plasmodium, Physiology, [SDV]Life Sciences [q-bio], Plasmodium vivax, Plant Science, Genome, Zoonosis, 0302 clinical medicine, Structural Biology, Zoonoses, Parasite hosting, Biology (General), Phylogeny, Genetics, 0303 health sciences, biology, Phylogenetic tree, Plasmodium simium, 3. Good health, [SDV] Life Sciences [q-bio], General Agricultural and Biological Sciences, Biotechnology, Research Article, Primates, QH301-705.5, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, parasitic diseases, medicine, Animals, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, Cell Biology, biology.organism_classification, medicine.disease, Malaria, Carrier Proteins, 030217 neurology & neurosurgery, Developmental Biology
Abstract: Background Plasmodium simium, a malaria parasite of non-human primates (NHP), was recently shown to cause zoonotic infections in humans in Brazil. We sequenced the P. simium genome to investigate its evolutionary history and to identify any genetic adaptions that may underlie the ability of this parasite to switch between host species. Results Phylogenetic analyses based on whole genome sequences of P. simium from humans and NHPs reveals that P. simium is monophyletic within the broader diversity of South American Plasmodium vivax, suggesting P. simium first infected NHPs as a result of a host switch of P. vivax from humans. The P. simium isolates show the closest relationship to Mexican P. vivax isolates. Analysis of erythrocyte invasion genes reveals differences between P. vivax and P. simium, including large deletions in the Duffy-binding protein 1 (DBP1) and reticulocyte-binding protein 2a genes of P. simium. Analysis of P. simium isolated from NHPs and humans revealed a deletion of 38 amino acids in DBP1 present in all human-derived isolates, whereas NHP isolates were multi-allelic. Conclusions Analysis of the P. simium genome confirmed a close phylogenetic relationship between P. simium and P. vivax, and suggests a very recent American origin for P. simium. The presence of the DBP1 deletion in all human-derived isolates tested suggests that this deletion, in combination with other genetic changes in P. simium, may facilitate the invasion of human red blood cells and may explain, at least in part, the basis of the recent zoonotic infections.
Published: 2021

12. 2D and 3D Ruthenium Nanoparticle Covalent Assemblies for Phenyl Acetylene Hydrogenation

Author: Andrea Falqui, Beatriz María Illescas Martínez, Pierre Roblin, M. Rosa Axet, Philippe Serp, Thomas Theussl, Silverio Coco, Nazario Martín, Hervé Martinez, Yuanyuan Min, Pierre Lecante, María Barcenilla, Alberto Casu, Bruno F. Machado, Faqiang Leng, Laboratoire de chimie de coordination (LCC), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials (LSRE-LCM), Faculdade de Engenharia (LSRE-LCM), Universidade do Porto = University of Porto, Centre d'élaboration de matériaux et d'études structurales (CEMES), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), 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), Université de Pau et des Pays de l'Adour (UPPA), King Abdullah University of Science and Technology (KAUST), Universidad de Valladolid [Valladolid] (UVa), Departamento de Química Orgánica I, Facultad de Química, Universidad Complutense, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Instituto IMDEA Nanociencia [Madrid], Instituto Imdea Nanociencia, Centre National de la Recherche Scientifique (CNRS), Institut National Polytechnique (INP), ANR-16-CE07-0007,ICARE_1,Nanostrucutres métal@carbone innovante pour une catalyse durable(2016), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), 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, Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement - INRAE (FRANCE), Institut National des Sciences Appliquées de Toulouse - INSA (FRANCE), King Abdullah University of Science and Technology - KAUST (SAUDI ARABIA), Office National d'Etudes et Recherches Aérospatiales - ONERA (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Universidad Complutense de Madrid - UCM (SPAIN), Université de Pau et des Pays de l'Adour - UPPA (FRANCE), Universidade do Porto - UP (PORTUGAL), and Centre d'Elaboration de Matériaux et d'Etudes Structurales - CEMES (Toulouse, France)
Subjects: Triphenylene, chemistry.chemical_element, Nanoparticle, 010402 general chemistry, 01 natural sciences, Ruthenium, Catalysis, Styrene, Inorganic Chemistry, chemistry.chemical_compound, [CHIM.GENI]Chemical Sciences/Chemical engineering, Génie chimique, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Génie des procédés, Covalent assembly, 010405 organic chemistry, Combinatorial chemistry, Acetylene hydrogenation, 0104 chemical sciences, Metallic nanoparticles, chemistry, Phenylacetylene, Covalent bond, Selectivity, Confinement effect
Abstract: International audience; The bottom‐up covalent assembly of metallic nanoparticles (NP) represents one of the innovative tools in nanotechnology to build functional heterostructures, with the resulting assemblies showing superior collective properties over the individual NP for a broad range of applications. The ability to control the dimensionality of the assembly is one of the major challenges in designing and understanding these advanced materials. Here, two new organic linkers were used as building blocks in order to guide the organization of Ru NP into two‐ or three‐dimensional covalent assemblies. The use of a hexa‐adduct functionalized C60 leads to the formation of 3D networks of 2.2 nm Ru NP presenting an interparticle distance of 3.0 nm, and the use of a planar carboxylic acid triphenylene derivative allows the synthesis of 2D networks of 1.9 nm Ru NP with an interparticle distance of 3.1 nm. The Ru NP networks were found to be active catalysts for the selective hydrogenation of phenylacetylene, reaching good selectivity toward styrene. Overall, we demonstrated that catalyst performances are significantly affected by the dimensionality (2D vs. 3D) of the heterostructures, which can be rationalize based on confinement effects.
Published: 2020

13. Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate

Author: Piet Herdewijn, Philippe Marliere, Gilles Gasser, Pascal Röthlisberger, Marcel Hollenstein, Luigi Cavallo, Fabienne Levi-Acobas, Mohit Chawla, Marie Flamme, Romina Oliva, Chimie bioorganique des acides nucléiques - Bioorganic chemistry of nucleic acids, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), King Abdullah University of Science and Technology (KAUST), Universita degli studi di Napoli 'Parthenope' [Napoli], Institute of Chemistry for Life and Health Sciences (iCLeHS), Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Génopole [Evry], Université d'Évry-Val-d'Essonne (UEVE), Institut de biologie systémique et synthétique (ISSB), Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), The authors gratefully acknowledge financial support from Institut Pasteur. We thank Mr. Germain Niogret for his help for the preparation of the cover picture featuring this article. The start-up company DNA Script is acknowledged for help in the UPLC-MS analysis of the oligonucleotides. L.C. and M.C. acknowledge King Abdullah University of Science and Technology (KAUST) for support and the KAUST Supercomputing Laboratory for providing computational resources of the supercomputer Shaheen II. R.O. thanks MIUR-FFABR (Fondo per il Finanziamento Attività Base di Ricerca) for funding. This work was financially supported by an ERC Consolidator Grant PhotoMedMet to G.G. (GA 681679) and has received support under the program 'Investissements d’ Avenir' launched by the French Government and implemented by the ANR with the reference ANR-10-IDEX-0001-02 PSL (G.G.)., ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), European Project: 681679, H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC),681679,PhotoMedMet(2017), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Università degli Studi di Napoli 'Parthenope' = University of Naples (PARTHENOPE)
Subjects: 0301 basic medicine, Models, Molecular, Silver, Base pair, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, 01 natural sciences, Biochemistry, 03 medical and health sciences, Synthetic biology, chemistry.chemical_compound, Polyphosphates, Nucleotide, Base Pairing, Density Functional Theory, chemistry.chemical_classification, DNA synthesis, 010405 organic chemistry, General Medicine, DNA, Purine Nucleosides, Genetic code, Combinatorial chemistry, 0104 chemical sciences, 030104 developmental biology, chemistry, Biocatalysis, Genetic Code, Nucleoside triphosphate, Nucleic acid, Molecular Medicine
Abstract: International audience; The expansion of the genetic alphabet with additional, unnatural base pairs (UBPs) is an important and long-standing goal in synthetic biology. Nucleotides acting as ligands for the coordination of metal cations have advanced as promising candidates for such an expansion of the genetic alphabet. However, the inclusion of artificial metal base pairs in nucleic acids mainly relies on solid-phase synthesis approaches, and very little is known about polymerase-mediated synthesis. Herein, we report the selective and high yielding enzymatic construction of a silver-mediated base pair (dImC–AgI–dPurP) as well as a two-step protocol for the synthesis of DNA duplexes containing such an artificial metal base pair. Guided by DFT calculations, we also shed light into the mechanism of formation of this artificial base pair as well as into the structural and energetic preferences. The enzymatic synthesis of the dImC–AgI–dPurP artificial metal base pair provides valuable insights for the design of future, more potent systems aiming at expanding the genetic alphabet.
Published: 2020

14. Characterization of pressure fluctuations within a controlled-diffusion blade boundary layer using the equilibrium wall-modelled LES

Author: Radouan Boukharfane, Julien Bodart, Matteo Parsani, Institut Supérieur de l'Aéronautique et de l'Espace - ISAE-SUPAERO (FRANCE), King Abdullah University of Science and Technology - KAUST (SAUDI ARABIA), Département Aérodynamique Energétique et Propulsion - DAEP (Toulouse, France), King Abdullah University of Science and Technology (KAUST), Département Aérodynamique Energétique et Propulsion (DAEP), and Institut Supérieur de l'Aéronautique et de l'Espace (ISAE-SUPAERO)
Subjects: Airfoil, Leading edge, Mécanique des fluides, lcsh:Medicine, 02 engineering and technology, 01 natural sciences, Article, [SPI.MECA.MEFL]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Fluids mechanics [physics.class-ph], 010305 fluids & plasmas, Physics::Fluid Dynamics, symbols.namesake, 0203 mechanical engineering, 0103 physical sciences, Aeroacoustics, Trailing edge, lcsh:Science, Physics, 020301 aerospace & aeronautics, Multidisciplinary, Turbulence, Computational science, lcsh:R, Spectral density, Reynolds number, Mechanics, Mechanical engineering, Boundary layer, Aerospace engineering, Mach number, LES, Wall-Modelling, symbols, lcsh:Q
Abstract: In this study, the generation of airfoil trailing edge broadband noise that arises from the interaction of turbulent boundary layer with the airfoil trailing edge is investigated. The primary objectives of this work are: (i) to apply a wall-modelled large-eddy simulation (WMLES) approach to predict the flow of air passing a controlled-diffusion blade, and (ii) to study the blade broadband noise that is generated from the interaction of a turbulent boundary layer with a lifting surface trailing edge. This study is carried out for two values of the Mach number, $${{\rm Ma}}_{\infty } = 0.3$$Ma∞=0.3 and 0.5, two values of the chord Reynolds number, $${{\rm Re}}=8.30 \times 10^5$$Re=8.30×105 and $$2.29 \times 10^6$$2.29×106, and two angles of attack, AoA $$=4^\circ$$=4∘ and $$5^\circ$$5∘. To examine the influence of the grid resolution on aerodynamic and aeroacoustic quantities, we compare our results with experimental data available in the literature. We also compare our results with two in-house numerical solutions generated from two wall-resolved LES (WRLES) calculations, one of which has a DNS-like resolution. We show that WMLES accurately predicts the mean pressure coefficient distribution, velocity statistics (including the mean velocity), and the traces of Reynolds tensor components. Furthermore, we observe that the instantaneous flow structures computed by the WMLES resemble those found in the reference WMLES database, except near the leading edge region. Some of the differences observed in these structures are associated with tripping and the transition to a turbulence mechanism near the leading edge, which are significantly affected by the grid resolution. The aeroacoustic noise calculations indicate that the power spectral density profiles obtained using the WMLES compare well with the experimental data.
Published: 2020

15. Theileria parasites subvert E2F signaling to stimulate leukocyte proliferation

Author: Marie Chaussepied, Sally A. Madsen-Bouterse, Doron Ginsberg, Gordon Langsley, Sara Mfarrej, Malak Haidar, Lindsay M. Fry, Claudia Daubenberger, Richard P. Bishop, Kyle Tretina, Takaya Sakura, Joana C. Silva, Donald P. Knowles, Vishvanath Nene, Arnab Pain, University of Maryland School of Medicine, University of Maryland System, Laboratoire de Biologie Comparative des Apicomplexes [Paris], Université Paris Descartes - Faculté de Médecine (UPD5 Médecine), Université Paris Descartes - Paris 5 (UPD5)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Washington State University (WSU), King Abdullah University of Science and Technology (KAUST), United States Department of Agriculture (USDA), Weizmann Institute of Science [Rehovot, Israël], International Livestock Research Institute [CGIAR, Nairobi] (ILRI), International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Bar-Ilan University [Israël], Swiss Tropical and Public Health Institute [Basel], University of Basel (Unibas), This work was supported in part by the United States Department of Agriculture, Agricultural Research Service (USDA-ARS) (58-5348-4-013), by the Norman Borlaug Commemorative Research Initiative, an initiative between the Feed the Future program of the U.S. Agency for International Development (USAID) and USDA-ARS (58-5348-2-117 F), by the Department for International Development of the United Kingdom, by the Bill and Melinda Gates Foundation (OPP1078791), and by the National Institute of Allergy and Infectious Diseases (T32 AI007540-14, on Immunity and Infection). This work was also supported by the grant Labex ParaFrap (ANR‐11‐LABX‐0024) and core funding from INSERM and the CNRS awarded to GL and a CRG4 grant (URF/1/2610‐01‐01) from the Office for Sponsored Research (OSR) in King Abdullah University of Science and Technology (KAUST) award to AP and GL and the faculty baseline fund (BAS/1/1020‐01‐01) awarded to AP., ANR-11-LABX-0024,ParaFrap,Alliance française contre les maladies parasitaires(2011), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Bodescot, Myriam, and Laboratoires d'excellence - Alliance française contre les maladies parasitaires - - ParaFrap2011 - ANR-11-LABX-0024 - LABX - VALID
Subjects: 0301 basic medicine, lcsh:Medicine, Article, Cell Line, 03 medical and health sciences, 0302 clinical medicine, Theileria, Leukocytes, Leukocyte proliferation, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, E2F, lcsh:Science, Data mining, Cell Proliferation, Multidisciplinary, biology, Cell growth, Intracellular parasite, lcsh:R, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], biology.organism_classification, 3. Good health, Cell biology, E2F Transcription Factors, 030104 developmental biology, [SDV.BBM.MN] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Cell culture, lcsh:Q, Signal transduction, 030217 neurology & neurosurgery, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, E2F1 Transcription Factor, Signal Transduction, Parasite host response
Abstract: Intracellular pathogens have evolved intricate mechanisms to subvert host cell signaling pathways and ensure their own propagation. A lineage of the protozoan parasite genus Theileria infects bovine leukocytes and induces their uncontrolled proliferation causing a leukemia-like disease. Given the importance of E2F transcription factors in mammalian cell cycle regulation, we investigated the role of E2F signaling in Theileria-induced host cell proliferation. Using comparative genomics and surface plasmon resonance, we identified parasite-derived peptides that have the sequence-specific ability to increase E2F signaling by binding E2F negative regulator Retinoblastoma-1 (RB). Using these peptides as a tool to probe host E2F signaling, we show that the disruption of RB complexes ex vivo leads to activation of E2F-driven transcription and increased leukocyte proliferation in an infection-dependent manner. This result is consistent with existing models and, together, they support a critical role of E2F signaling for Theileria-induced host cell proliferation, and its potential direct manipulation by one or more parasite proteins.
Published: 2020

16. CATION-CHLORIDE CO-TRANSPORTER 1 (CCC1) Mediates Plant Resistance against Pseudomonas syringae

Author: Jianing Mi, M. Rob G. Roelfsema, Heribert Hirt, Guoxin Cui, Salim Al-Babili, Baoda Han, Julien Sechet, Manuel Aranda, Yunhe Jiang, Grégory Mouille, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST)-King Abdullah University of Science and Technology (KAUST), Department of Molecular Plant Physiology and Biophysics, Biocenter University of Würzburg = Biozentrum der Universität Würzburg, Julius-Maximilians-Universität Würzburg (JMU)-Julius-Maximilians-Universität Würzburg (JMU), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Perutz Laboratories, University of Vienna [Vienna], Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), King Abdullah University of Science & Technology BAS/01/1062-01-01 URF/1/2965, European Commission 267196, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU)-Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Triggered Immunity, Physiology, Antimicrobial peptides, Plant Immunity, Plant Science, Trans-golgi Network, 01 natural sciences, Pv. Tomato Dc3000, Arabidopsis-thaliana, Arabidopsis, Metabolic Gene Clusters, Genetics, Camalexin, Pseudomonas syringae, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Lipid Transfer Proteins, Acyl-coenzyme, biology, Chemistry, fungi, food and beverages, Depolarization, biology.organism_classification, Cell biology, Disease Susceptibility, Cotransporter, Pathogenesis-related Proteins, 010606 plant biology & botany, Transcription Factors
Abstract: International audience; Plasma membrane (PM) depolarization functions as an initial step in plant defense signaling pathways. However, only a few ion channels/transporters have been characterized in the context of plant immunity. Here, we show that the Arabidopsis (Arabidopsis thaliana) Na+:K+:2Cl(-) (NKCC) cotransporter CCC1 has a dual function in plant immunity. CCC1 functions independently of PM depolarization and negatively regulates pathogen-associated molecular pattern-triggered immunity. However, CCC1 positively regulates plant basal and effector-triggered resistance to Pseudomonas syringae pv. tomato (Pst) DC3000. In line with the compromised immunity to Pst DC3000, ccc1 mutants show reduced expression of genes encoding enzymes involved in the biosynthesis of antimicrobial peptides, camalexin, and 4-OH-ICN, as well as pathogenesis-related proteins. Moreover, genes involved in cell wall and cuticle biosynthesis are constitutively down-regulated in ccc1 mutants, and the cell walls of these mutants exhibit major changes in monosaccharide composition. The role of CCC1 ion transporter activity in the regulation of plant immunity is corroborated by experiments using the specific NKCC inhibitor bumetanide. These results reveal a function for ion transporters in immunity-related cell wall fortification and antimicrobial biosynthesis.
Published: 2020

17. The Red Sea Deep Water is a potent source of atmospheric ethane and propane

Author: Ivan Tadic, Sergey Osipov, Horst Fischer, Jean-Daniel Paris, Tobias Könemann, Achim Edtbauer, Eva Y. Pfannerstill, Jonathan Williams, T. Sattler, Nijing Wang, David Walter, Andrea Pozzer, Christof Stönner, Lisa Ernle, Jos Lelieveld, V.N. Matthaios, Efstratios Bourtsoukidis, Max Planck Institute for Chemistry (MPIC), Max-Planck-Gesellschaft, School of Geography, Earth and Environmental Sciences [Birmingham], University of Birmingham [Birmingham], Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ICOS-RAMCES (ICOS-RAMCES), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Biogeochemistry (MPI-BGC), The Cyprus Institute, Energy, Environment and Water Research Center, H2020 Marie Skłodowska-Curie Actions, MSCA: 674911 King Abdullah University of Science and Technology, KAUST Kuwait Institute for Scientific Research, KISR Horizon 2020 Framework Programme, H2020: 856612, We acknowledge the fruitful collaborations with the Cyprus Institute (CyI), the King Abdullah University of Science and Technology (KAUST), and the Kuwait Institute for Scientific Research (KISR). We are grateful to Hays Ships Ltd, the ship’s captain Pavel Kirzner, and the ship crew for providing the best possible working conditions onboard Kommandor Iona. We thank all the participants of the AQABA ship campaign and in particular Hartwig Harder for the fruitful discussions and day-to-day organization of the campaign, and Marcel Dorf, Claus Koeppel, Thomas Klüpfel, and Rolf Hofmann for logistics organization and assistance during the setup phase. Uwe Parchatka is acknowledged for his contribution to the NOx data set. Marc Delmotte, Laurence Vialettes, and Olivier Laurent are acknowledged for helping with setting up the methane measurements. NW acknowledges funding by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 674911. We acknowledge the EMME-CARE project from the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement No. 856612), as well as matching co-funding by the Government of the Republic of Cyprus., European Project: 674911,H2020,H2020-MSCA-ITN-2015,IMPACT(2016), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), and Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)
Subjects: Atmospheric chemistry, 010504 meteorology & atmospheric sciences, Atmospheric circulation, Science, [SDV]Life Sciences [q-bio], General Physics and Astronomy, 010501 environmental sciences, Atmospheric sciences, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Article, Environmental impact, chemistry.chemical_compound, Propane, Hotspot (geology), 14. Life underwater, Tropospheric ozone, Underwater, lcsh:Science, 0105 earth and related environmental sciences, chemistry.chemical_classification, Pollutant, Multidisciplinary, Environmental monitoring, General Chemistry, 6. Clean water, Hydrocarbon, chemistry, Marine chemistry, 13. Climate action, lcsh:Q
Abstract: Non-methane hydrocarbons (NMHCs) such as ethane and propane are significant atmospheric pollutants and precursors of tropospheric ozone, while the Middle East is a global emission hotspot due to extensive oil and gas production. Here we compare in situ hydrocarbon measurements, performed around the Arabian Peninsula, with global model simulations that include current emission inventories (EDGAR) and state-of-the-art atmospheric circulation and chemistry mechanisms (EMAC model). While measurements of high mixing ratios over the Arabian Gulf are adequately simulated, strong underprediction by the model was found over the northern Red Sea. By examining the individual sources in the model and by utilizing air mass back-trajectory investigations and Positive Matrix Factorization (PMF) analysis, we deduce that Red Sea Deep Water (RSDW) is an unexpected, potent source of atmospheric NMHCs. This overlooked underwater source is comparable with total anthropogenic emissions from entire Middle Eastern countries, and significantly impacts the regional atmospheric chemistry., The Middle East is known to emit large amounts of non-methane hydrocarbon pollutants to the atmosphere, but the sources are poorly characterized. Here the authors discover a new source—deep water in the Red Sea—and calculate that its emissions exceed rates of several high gas-production countries.
Published: 2020

18. 3D Ruthenium Nanoparticle Covalent Assemblies from Polymantane Ligands for Confined Catalysis

Author: Philippe Serp, Pierre Roblin, Yann Tison, Hervé Martinez, Pierre Lecante, Andrea Falqui, Yuanyuan Min, Iker del Rosal, Romuald Poteau, Jean-Cyrille Hierso, Didier Poinsot, M. Rosa Axet, H. Nasrallah, Iann C. Gerber, Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement - INRAE (FRANCE), Institut National des Sciences Appliquées de Toulouse - INSA (FRANCE), Institut National de la Santé et de la Recherche Médicale - INSERM (FRANCE), King Abdullah University of Science and Technology - KAUST (SAUDI ARABIA), Office National d'Etudes et Recherches Aérospatiales - ONERA (FRANCE), Université de Bourgogne - UB (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Université de Pau et des Pays de l'Adour - UPPA (FRANCE), Laboratoire de Physique et Chimie des Nano-Objets - LPCNO (Toulouse, France), Laboratoire de chimie de coordination (LCC), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] (ICMUB), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC), Centre d'élaboration de matériaux et d'études structurales (CEMES), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Université de Pau et des Pays de l'Adour (UPPA), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génie Chimique (LGC), 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, King Abdullah University of Science and Technology (KAUST), Laboratoire de physique et chimie des nano-objets (LPCNO), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-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 des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), 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), Université de Toulouse (UT)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), CNRS, Université de Bourgogne, Conseil Régional de Bourgogne (plan d'actions régional pour l’innovation PARI), Fonds européen de développement régional (FEDER programs), and ANR-16-CE07-0007,ICARE_1,Nanostrucutres métal@carbone innovante pour une catalyse durable(2016)
Subjects: General Chemical Engineering, Carboxylic acid, chemistry.chemical_element, Nanoparticle, 02 engineering and technology, 010402 general chemistry, Ligands, 01 natural sciences, Catalysis, chemistry.chemical_compound, [CHIM.GENI]Chemical Sciences/Chemical engineering, Organic acids, Materials Chemistry, Génie chimique, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Amines, Génie des procédés, chemistry.chemical_classification, Catalysts, Ligand, Decarbonylation, General Chemistry, 021001 nanoscience & nanotechnology, Combinatorial chemistry, 0104 chemical sciences, Ruthenium, chemistry, Phenylacetylene, Metals, Density functional theory, 0210 nano-technology
Abstract: International audience; The synthesis of metal nanoparticle (NP) assemblies stabilized by functional molecules is an important research topic in nanoscience, and the ability to control interparticle distances and positions in NP assemblies is one of the major challenges in designing and understanding functional nanostructures. Here, two series of functionalized adamantanes, bis-adamantanes, and diamantanes, bearing carboxylic acid or amine functional groups, were used as building blocks to produce, via a straightforward method, networks of ruthenium NPs. Both the nature of the ligand and the Ru/ligand ratio affect the interparticle distance in the assemblies. The use of 1,3-adamantanedicarboxylic acid allows the synthesis of three-dimensional (3D) networks of 1.7–1.9 nm Ru NPs presenting an interparticle distance of 2.5–2.7 nm. The surface interaction between Ru NPs and the ligands was investigated spectroscopically using a 13C-labeled ligand, as well as theoretically with density functional theory (DFT) calculations. We found that Ru species formed during the NP assembly are able to partially decarbonylate carboxylic acid ligands at room temperature. Decarbonylation of a carboxylic acid at room temperature in the presence of dihydrogen usually occurs on catalysts at much higher temperatures and pressures. This result reveals a very high reactivity of ruthenium species formed during the network assembly. The Ru NP networks were found to be active catalysts for the selective hydrogenation of phenylacetylene, reaching good selectivity toward styrene. Overall, we demonstrated that catalyst activity, selectivity, and NP network stability are significantly affected by Ru NP interparticle distance and electronic ligand effects. As such, these materials constitute a unique set that should allow a better understanding of the complex surface chemistry in carbon-supported metal catalysts.
Published: 2020

19. Spatial hierarchical modeling of threshold exceedances using rate mixtures

Author: Thomas Opitz, Raphaël Huser, Rishikesh Yadav, King Abdullah University of Science and Technology (KAUST), Biostatistique et Processus Spatiaux (BioSP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) OSR-CRG2017-3434
Subjects: Statistics and Probability, FOS: Computer and information sciences, precipitation extremes, 010504 meteorology & atmospheric sciences, Computer science, 01 natural sciences, extended generalized Pareto distribution, Methodology (stat.ME), 010104 statistics & probability, symbols.namesake, Bayesian hierarchical modeling, 0101 mathematics, extreme event, Statistics - Methodology, 0105 earth and related environmental sciences, penalized complexity prior, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Information retrieval, Hierarchical modeling, Ecological Modeling, Markov chain Monte Carlo, Associate editor, Work (electrical), symbols
Abstract: International audience; We develop new flexible univariate models for light-tailed and heavy-tailed data, which extend a hierarchical representation of the generalized Pareto (GP) limit for threshold exceedances. These models can accommodate departure from asymptotic threshold stability in finite samples while keeping the asymptotic GP distribution as a special (or boundary) case and can capture the tails and the bulk jointly without losing much flexibility. Spatial dependence is modeled through a latent process, while the data are assumed to be conditionally independent. Focusing on a gamma-gamma model construction, we design penalized complexity priors for crucial model parameters, shrinking our proposed spatial Bayesian hierarchical model toward a simpler reference whose marginal distributions are GP with moderately heavy tails. Our model can be fitted in fairly high dimensions using Markov chain Monte Carlo by exploiting the Metropolis-adjusted Langevin algorithm (MALA), which guarantees fast convergence of Markov chains with efficient block proposals for the latent variables. We also develop an adaptive scheme to calibrate the MALA tuning parameters. Moreover, our model avoids the expensive numerical evaluations of multifold integrals in censored likelihood expressions. We demonstrate our new methodology by simulation and application to a dataset of extreme rainfall events that occurred in Germany. Our fitted gamma-gamma model provides a satisfactory performance and can be successfully used to predict rainfall extremes at unobserved locations.
Published: 2020

20. Accelerated Dimension-Independent Adaptive Metropolis

Author: Ltaief, Hatem [King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia]
Published: 2016
Full Text: View/download PDF

21. Multilevel ensemble Kalman filtering

Author: Tempone, Raul [King Abdullah University of Science and Technology (KAUST), Thuwal (Saudi Arabia)]
Published: 2016
Full Text: View/download PDF

22. Processus et catalyseurs complexes supportés pour l'oxydation et/ou l'ammoxydation d'oléfines; leur procédé de preparation

Author: Barman, Samir, Samantaray, Manoja Kumar, Saih, Youssef, Basset, Jean-Marie, Hammad, Edy Abou, Taoufik, Mostafa, Merle, Nicolas, Szeto, Kai Chung, Le Quemener, Frédéric, de Mallmann, Aimery, Université de Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, Unité de Catalyse et Chimie du Solide (UCCS) - UMR 8181, King Abdullah University of Science and Technology [KAUST], Laboratoire de Chimie, Catalyse, Polymères et Procédés, R 5265 [C2P2], King Abdullah University of Science and Technology (KAUST), Laboratoire de Chimie, Catalyse, Polymères et Procédés, R 5265 (C2P2), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Unité de Catalyse et Chimie du Solide - UMR 8181 (UCCS), and Université d'Artois (UA)-Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: [CHIM.CATA]Chemical Sciences/Catalysis
Abstract: Embodiments of the present disclosure describe a catalyst and/or a precatalyst, in particular a single site catalyst and/or a single site precatalyst, for the oxidation and/or ammoxidation of olefins to produce aldehydes and/or nitriles, methods of preparing a corresponding catalyst and/or precatalyst, in particular single site catalyst and/or single site precatalyst, and methods of using said catalyst and/or precatalyst, in particular said single site catalyst and/or single site precatalyst, to produce aldehydes and/or nitriles.; Des modes de réalisation de la présente invention concernent un catalyseur et/ou un pré-catalyseur, en particulier un catalyseur à site unique et/ou un pré-catalyseur à site unique, pour l'oxydation et/ou l'ammoxydation d'oléfines pour produire des aldéhydes et/ou des nitriles, des procédés de préparation d'un catalyseur et/ou d'un pré-catalyseur correspondants, en particulier un catalyseur à site unique et/ou un pré-catalyseur à site unique, et des procédés d'utilisation dudit catalyseur et/ou de pré-catalyseur, en particulier dudit catalyseur à site unique et/ou de pré-catalyseur à site unique, pour produire des aldéhydes et/ou des nitriles.
Published: 2019

23. MAP4K4 associates with BIK1 to regulate plant innate immunity

Author: Baoda Han, Jean Colcombet, Huoming Zhang, Kiruthiga Mariappan, Yunhe Jiang, Jean Bigeard, Heribert Hirt, King Abdullah University of Science and Technology (KAUST), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Sorbonne Paris Cité (COMUE) (USPC), Max F. Perutz Laboratories, University of Vienna [Vienna]-Department of Chemistry, King Abdullah University of Science and Technology (KAUST). Grant Numbers : BAS/1/1062‐01‐01, URF/1/2965‐01‐01, Institut National de la Recherche Agronomique (INRA). Grant Number: ANR‐10‐LABX‐0040‐SPS, Centre National de la Recherche Scientifique (CNRS). Grant Number: ANR‐10‐LABX‐0040‐SPS, and LabEx Saclay Plant Sciences‐SPS.
Subjects: Engineering, Proteasome Endopeptidase Complex, animal structures, [SDV]Life Sciences [q-bio], Protein Serine-Threonine Kinases, Biochemistry, Models, Biological, 03 medical and health sciences, 0302 clinical medicine, Gene Expression Regulation, Plant, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Immunity, Amino Acid Sequence, Phosphorylation, Molecular Biology, Conserved Sequence, 030304 developmental biology, Disease Resistance, Plant Diseases, Cognitive science, 0303 health sciences, Innate immune system, business.industry, PP2C38, fungi, Cell Membrane, BIK1, Articles, Plants, Protein Transport, Genetic Loci, Flg22-triggered immunity, Mutation, Proteolysis, Cytokines, business, Reactive Oxygen Species, 030217 neurology & neurosurgery, Protein Binding, Signal Transduction, MAP4K4
Abstract: King Abdullah University of Science and Technology (KAUST). Grant Numbers: BAS/1/1062‐01‐01, URF/1/2965‐01‐01 Institut National de la Recherche Agronomique (INRA). Grant Number: ANR‐10‐LABX‐0040‐SPS Centre National de la Recherche Scientifique (CNRS). Grant Number: ANR‐10‐LABX‐0040‐SPS LabEx Saclay Plant Sciences‐SPS; International audience; To perceive pathogens, plants employ pattern recognition receptor (PRR) complexes, which then transmit these signals via the receptor-like cytoplasmic kinase BIK1 to induce defense responses. How BIK1 activity and stability are controlled is still not completely understood. Here, we show that the Hippo/STE20 homolog MAP4K4 regulates BIK1-mediated immune responses. MAP4K4 associates and phosphorylates BIK1 at Ser233, Ser236, and Thr242 to ensure BIK1 stability and activity. Furthermore, MAP4K4 phosphorylates PP2C38 at Ser77 to enable flg22-induced BIK1 activation. Our results uncover that a Hippo/STE20 homolog, MAP4K4, maintains the homeostasis of the central immune component BIK1.
Published: 2019

24. Changes in the Arabidopsis RNA-binding proteome reveal novel stress response mechanisms

Author: Kathryn S. Lilley, Christoph A Gehring, Ludivine Thomas, Claudius Marondedze, Physiologie cellulaire et végétale (LPCV), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-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), University of Cambridge [UK] (CAM), King Abdullah University of Science and Technology (KAUST), HM. CLAUSE [France], Università degli Studi di Perugia (UNIPG), Univ Cambridge, Dept Biochem, Cambridge CB2 1GA, England, affiliation inconnue, Office of Competitive Research Grant Program, King Abdullah University of Science and Technology (KAUST) CRG3-62140383, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Università degli Studi di Perugia = University of Perugia (UNIPG), Marondedze, Claudius [0000-0002-2113-904X], and Apollo - University of Cambridge Repository
Subjects: 0106 biological sciences, 0301 basic medicine, Proteomics, Drought stress, Proteome, mRNA interactomics, Arabidopsis thaliana, Arabidopsis, Systems analysis, RNA-binding protein, RNA-binding proteins, Plant Science, Biology, 01 natural sciences, Interactome, 03 medical and health sciences, Plant Growth Regulators, Stress, Physiological, lcsh:Botany, Gene expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, RNA, Messenger, Gene, 2. Zero hunger, Messenger RNA, Mass spectrometry, Arabidopsis Proteins, RNA, Adaptation, Physiological, Cell biology, lcsh:QK1-989, 030104 developmental biology, RNA, Plant, 010606 plant biology & botany, Research Article, Abscisic Acid
Abstract: Background RNA-binding proteins (RBPs) are increasingly recognized as regulatory component of post-transcriptional gene expression. RBPs interact with mRNAs via RNA-binding domains and these interactions affect RNA availability for translation, RNA stability and turn-over thus affecting both RNA and protein expression essential for developmental and stimulus specific responses. Here we investigate the effect of severe drought stress on the RNA-binding proteome to gain insights into the mechanisms that govern drought stress responses at the systems level. Results Label-free mass spectrometry enabled the identification 567 proteins of which 150 significantly responded to the drought-induced treatment. A gene ontology analysis revealed enrichment in the “RNA binding” and “RNA processing” categories as well as biological processes such as “response to abscisic acid” and “response to water deprivation”. Importantly, a large number of the stress responsive proteins have not previously been identified as RBPs and include proteins in carbohydrate metabolism and in the glycolytic and citric acid pathways in particular. This suggests that RBPs have hitherto unknown roles in processes that govern metabolic changes during stress responses. Furthermore, a comparative analysis of RBP domain architectures shows both, plant specific and common domain architectures between plants and animals. The latter could be an indication that RBPs are part of an ancient stress response. Conclusion This study establishes mRNA interactome capture technique as an approach to study stress signal responses implicated in environmental changes. Our findings denote RBP changes in the proteome as critical components in plant adaptation to changing environments and in particular drought stress protein-dependent changes in RNA metabolism. Electronic supplementary material The online version of this article (10.1186/s12870-019-1750-x) contains supplementary material, which is available to authorized users.
Published: 2019

25. Large Intercalation Pseudocapacitance in 2D VO2(B): Breaking through the Kinetic Barrier

Author: Husam N. Alshareef, Chuan Xia, Yungang Zhou, Chao Zhao, Zhiguo Wang, Patrick Rozier, Zifeng Lin, Hanfeng Liang, Centre National de la Recherche Scientifique - CNRS (FRANCE), Collège de France (FRANCE), Ecole Nationale Supérieure de Chimie de Paris - ENSCP (FRANCE), Ecole Nationale Supérieure de Chimie de Montpellier - ENSCM (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut polytechnique de Grenoble (FRANCE), King Abdullah University of Science and Technology - KAUST (SAUDI ARABIA), Sorbonne Université (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Université de Nantes (FRANCE), Université de Picardie Jules Verne (FRANCE), Université de Pau et des Pays de l'Adour - UPPA (FRANCE), University of Electronic Science and Technology of China - UESTC (CHINA), Université de Haute Alsace - UHA (FRANCE), Université de Montpellier (FRANCE), Centre Interuniversitaire de Recherche et d'Ingénierie des Matériaux - CIRIMAT (Toulouse, France), King Abdullah University of Science and Technology (KAUST), Centre interuniversitaire de recherche et d'ingenierie des matériaux (CIRIMAT), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Réseau sur le stockage électrochimique de l'énergie (RS2E), Université de Nantes (UN)-Aix Marseille Université (AMU)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Collège de France (CdF (institution))-Université de Picardie Jules Verne (UPJV)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA), University of Electronic Science and Technology of China [Chengdu] (UESTC), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC), Université de Picardie Jules Verne (UPJV)-Institut de Chimie du CNRS (INC)-Aix Marseille Université (AMU)-Université de Pau et des Pays de l'Adour (UPPA)-Université de Nantes (UN)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Collège de France (CdF (institution))-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Université Grenoble Alpes (UGA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), University of Electronic Science and Technology of China (UESTC), and Institut National Polytechnique de Toulouse - INPT (FRANCE)
Subjects: Energie électrique, Materials science, Nanostructure, Matériaux, Kinetics, Intercalation (chemistry), 02 engineering and technology, 010402 general chemistry, Kinetic energy, 01 natural sciences, Pseudocapacitance, Ion, [SPI.MAT]Engineering Sciences [physics]/Materials, symbols.namesake, Intercalation, General Materials Science, 2D, Mechanical Engineering, [SPI.NRJ]Engineering Sciences [physics]/Electric power, Interaction energy, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Ultrathin, Kinetic barrier, Mechanics of Materials, Chemical physics, symbols, van der Waals force, 0210 nano-technology
Abstract: International audience; VO2 (B) features two lithiation/delithiation processes, one of which is kinetically facile and has been commonly observed at 2.5 V versus Li/Li+ in various VO2 (B) structures. In contrast, the other process, which occurs at 2.1 V versus Li/Li+, has only been observed at elevated temperatures due to large interaction energy barrier and extremely sluggish kinetics. Here, it is demonstrated that a rational design of atomically thin, 2D nanostructures of VO2 (B) greatly lowers the interaction energy and Li+‐diffusion barrier. Consequently, the kinetically sluggish step is successfully enabled to proceed at room temperature for the first time ever. The atomically thin 2D VO2 (B) exhibits fast charge storage kinetics and enables fully reversible uptake and removal of Li ions from VO2 (B) lattice without a phase change, resulting in exceptionally high performance. This work presents an effective strategy to speed up intrinsically sluggish processes in non‐van der Waals layered materials.
Published: 2018

26. Full-likelihood inference for max-stable processes

Author: Dombry, Clément, Genton, Marc G., Huser, Raphaël, Ribatet, Mathieu, Laboratoire de Mathématiques de Besançon ( LMB ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), King Abdullah University of Science and Technology ( KAUST ), Computer, Electrical and Mathematical Sciences and Engineering Division, Institut Montpelliérain Alexander Grothendieck ( IMAG ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Mathématiques de Besançon (UMR 6623) (LMB), Université de Bourgogne (UB)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), King Abdullah University of Science and Technology (KAUST), Institut Montpelliérain Alexander Grothendieck (IMAG), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], [ MATH.MATH-ST ] Mathematics [math]/Statistics [math.ST]
Published: 2018

27. Random matrix-improved kernels for large dimensional spectral clustering

Author: Romain Couillet, Abla Kammoun, Hafiz Tiomoko Ali, Laboratoire des signaux et systèmes (L2S), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), King Abdullah University of Science and Technology (KAUST), NXP Semiconductors, Laboratoire des signaux et systèmes ( L2S ), Université Paris-Sud - Paris 11 ( UP11 ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ), and King Abdullah University of Science and Technology ( KAUST )
Subjects: business.industry, Computer science, 020206 networking & telecommunications, Pattern recognition, Context (language use), 02 engineering and technology, 01 natural sciences, Spectral clustering, [ INFO.INFO-LG ] Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], 010104 statistics & probability, Kernel method, ComputingMethodologies_PATTERNRECOGNITION, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], 0202 electrical engineering, electronic engineering, information engineering, Artificial intelligence, [ MATH.MATH-ST ] Mathematics [math]/Statistics [math.ST], 0101 mathematics, business, Cluster analysis, [ INFO.INFO-AI ] Computer Science [cs]/Artificial Intelligence [cs.AI], Random matrix, MNIST database
Abstract: International audience; Leveraging on recent random matrix advances in the performance analysis of kernel methods for classification and clustering, this article proposes a new family of kernel functions theoretically largely outperforming standard kernels in the context of asymp-totically large and numerous datasets. These kernels are designed to discriminate statistical means and covariances across data classes at a theoretically minimal rate (with respect to data size). Applied to spectral clustering, we demonstrate the validity of our theoretical findings both on synthetic and real-world datasets (here, the popular MNIST database as well as EEG recordings on epileptic patients). Index Terms— Spectral clustering, inner product kernels, random matrix theory.
Published: 2018

28. Random Matrix Asymptotics of Inner Product Kernel Spectral Clustering

Author: Romain Couillet, Hafiz Tiomoko Ali, Abla Kammoun, Laboratoire des signaux et systèmes ( L2S ), Université Paris-Sud - Paris 11 ( UP11 ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ), King Abdullah University of Science and Technology ( KAUST ), NXP Semiconductors, Laboratoire des signaux et systèmes (L2S), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), and King Abdullah University of Science and Technology (KAUST)
Subjects: Gaussian, 02 engineering and technology, random matrix theory, Index Terms— Spectral clustering, random matrices, 01 natural sciences, [ INFO.INFO-LG ] Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], 010104 statistics & probability, symbols.namesake, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], 0202 electrical engineering, electronic engineering, information engineering, inner product kernels, Symmetric matrix, [ MATH.MATH-ST ] Mathematics [math]/Statistics [math.ST], Statistical physics, 0101 mathematics, [ INFO.INFO-AI ] Computer Science [cs]/Artificial Intelligence [cs.AI], Cluster analysis, Eigenvalues and eigenvectors, Mathematics, 020206 networking & telecommunications, 16. Peace & justice, Mixture model, Spectral clustering, Kernel (statistics), symbols, Random matrix
Abstract: International audience; We study in this article the asymptotic performance of spectral clustering with inner product kernel for Gaussian mixture models of high dimension with numerous samples. As is now classical in large dimensional spectral analysis, we establish a phase transition phenomenon by which a minimum distance between the class means and covariances is required for clustering to be possible from the dominant eigenvectors. Beyond this phase transition, we evaluate the asymptotic content of the dominant eigenvectors thus allowing for a full characterization of clustering performance. However, a surprising finding is that in some particular scenarios, the phase transition does not occur and clustering can be achieved irrespective of the class means and covariances. This is evidenced here in the case of the mixture of two Gaussian datasets having the same means and arbitrary difference between covariances.
Published: 2018

29. miR-126-5p by direct targeting of JNK- interacting protein-2 (JIP-2) plays a key role in Theileria-infected macrophage virulence

Author: Perle Latré de Laté, Shahin Tajeri, Malak Haidar, Gordon Langsley, Arnab Pain, Hifzur Rahman Ansari, Zineb Rchiad, Fathia Ben-Rached, Pathogen Genomics Laboratory [Thuwal, Arabie saoudite], Biological and Environmental Sciences and Engineering Division [Thuwal, Arabie saoudite] (BESE), King Abdullah University of Science and Technology (KAUST)-King Abdullah University of Science and Technology (KAUST), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Cellulaire Comparative des Apicomplexes [Paris], Université Paris Descartes - Paris 5 (UPD5), Global Station for Zoonosis Control [Sapporo, Japon] (GSZ), Global Institution for Collaborative Research and Education [Sapporo, Japon] (GI-CoRE), Hokkaido University [Sapporo, Japan]-Hokkaido University [Sapporo, Japan], This study was supported by the Competitive Research Grant (OSR-2015-CRG4-2610) from the Office for Sponsored Research (OSR, https://osr.kaust.edu.sa/crf/Funding/Pages/CRFCRG.aspx) in King Abdullah University of Science and Technology (KAUST)., and Bodescot, Myriam
Subjects: 0301 basic medicine, B Cells, MAP Kinase Kinase 4, Biochemistry, White Blood Cells, chemistry.chemical_compound, Aromatic Amino Acids, Animal Cells, Theileria, Medicine and Health Sciences, Post-Translational Modification, Phosphorylation, Amino Acids, Tyrosine, lcsh:QH301-705.5, Cells, Cultured, Virulence, Organic Compounds, Transfection, Precipitation Techniques, 3. Good health, Cell biology, Nucleic acids, Chemistry, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Physical Sciences, [SDV.IMM]Life Sciences [q-bio]/Immunology, GRB2, Cellular Types, Research Article, lcsh:Immunologic diseases. Allergy, [SDV.IMM] Life Sciences [q-bio]/Immunology, Immune Cells, Immunology, Biology, Research and Analysis Methods, Microbiology, 03 medical and health sciences, Downregulation and upregulation, Hydroxyl Amino Acids, Virology, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Genetics, Immunoprecipitation, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Non-coding RNA, Antibody-Producing Cells, Molecular Biology Techniques, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Molecular Biology, Adaptor Proteins, Signal Transducing, Blood Cells, Macrophages, Organic Chemistry, Chemical Compounds, Biology and Life Sciences, Proteins, Tyrosine phosphorylation, Cell Biology, biology.organism_classification, Theileria annulata, Gene regulation, Theileriasis, Transcription Factor AP-1, MicroRNAs, 030104 developmental biology, lcsh:Biology (General), chemistry, biology.protein, RNA, Cattle, Parasitology, Gene expression, lcsh:RC581-607
Abstract: Theileria annulata is an apicomplexan parasite that infects and transforms bovine macrophages that disseminate throughout the animal causing a leukaemia-like disease called tropical theileriosis. Using deep RNAseq of T. annulata-infected B cells and macrophages we identify a set of microRNAs induced by infection, whose expression diminishes upon loss of the hyper-disseminating phenotype of virulent transformed macrophages. We describe how infection-induced upregulation of miR-126-5p ablates JIP-2 expression to release cytosolic JNK to translocate to the nucleus and trans-activate AP-1-driven transcription of mmp9 to promote tumour dissemination. In non-disseminating attenuated macrophages miR-126-5p levels drop, JIP-2 levels increase, JNK1 is retained in the cytosol leading to decreased c-Jun phosphorylation and dampened AP-1-driven mmp9 transcription. We show that variation in miR-126-5p levels depends on the tyrosine phosphorylation status of AGO2 that is regulated by Grb2-recruitment of PTP1B. In attenuated macrophages Grb2 levels drop resulting in less PTP1B recruitment, greater AGO2 phosphorylation, less miR-126-5p associated with AGO2 and a consequent rise in JIP-2 levels. Changes in miR-126-5p levels therefore, underpin both the virulent hyper-dissemination and the attenuated dissemination of T. annulata-infected macrophages., Author summary Theileria annulata-infected bovine macrophages lose their hyper-disseminating virulent phenotype during long-term culture and are used as attenuated live vaccines to fight tropical theileriosis. Deep microRNA sequencing revealed that infection of both B cells and macrophages alters the expression of a large number of host cell microRNAs. We focused on miR-126-5p as its expression was induced by infection, but diminished in attenuated macrophages that had lost their disease causing disseminating phenotype. We show that miR-126-5p in virulent macrophages directly targets and suppresses a cytosolic scaffold protein called JNK-Interacting Protein-2 (JIP-2), so liberating JNK1 to enter the nucleus and phosphorylate c-Jun. This activates AP-1-driven transcription of mmp9 that promotes tumour dissemination. In virulent macrophages, an adaptor protein called Grb2 recruits the tyrosine phosphatase PTP1B to AGO2 so decreasing AGO2 phosphorylation to increase miR-126-5p levels. By contrast, in attenuated macrophages AGO2 tyrosine phosphorylation increases and miR-126-5p levels drop leading to a regain in JIP-2 expression that retains JNK1 in the cytosol. This leads to decreased nuclear c-Jun phosphorylation and reduced mmp9 production. Thus, variations in miR-126-5p levels underpin both virulent hyper-dissemination and attenuation of T. annulata-transfected macrophages.
Published: 2018

30. Ethylene induced plant stress tolerance by Enterobacter sp. SA187 is mediated by 2-keto-4-methylthiobutyric acid production

Author: Kiruthiga Mariappan, Axel de Zélicourt, Dominique Van Der Straeten, Thomas Depaepe, Moussa Benhamed, Heribert Hirt, Eleonora Rolli, Rewaa S. Jalal, Florence Guérard, Maged M. Saad, Ihsanullah Daur, Yakun Xie, Hanin S. Alzubaidy, Jean Colcombet, Lukas Synek, Cristina Andrés-Barrao, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Sorbonne Paris Cité (COMUE) (USPC), Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), King Abdulaziz University, Universiteit Gent = Ghent University (UGENT), King Abdullah University of Science and Technology (KAUST) BAS/1/1062-01-01, Agreenskills fellowship programme from the EU's Seventh Framework Programme FP7-609398., Universiteit Gent = Ghent University [Belgium] (UGENT), De Julien De Zelicourt, Axel, Synek, Lukas, Saad, Maged, and Hirt, Heribert
Subjects: 0106 biological sciences, 0301 basic medicine, Salinity, Cancer Research, Ethylene, [SDV]Life Sciences [q-bio], Arabidopsis, PROTEIN, Fractional Precipitation, Plant Science, Plant Roots, Biochemistry, Physical Chemistry, 01 natural sciences, chemistry.chemical_compound, Methionine, Gene Expression Regulation, Plant, SALINITY, Plant Resistance to Abiotic Stress, Arabidopsis thaliana, Plant Hormones, Genetics (clinical), GROWTH-PROMOTING RHIZOBACTERIA, 2. Zero hunger, Abiotic component, Ecology, biology, SALT-TOLERANCE, Organic Compounds, Plant Biochemistry, Salting Out, Plant Anatomy, Eukaryota, food and beverages, Agriculture, Plants, Adaptation, Physiological, Precipitation Techniques, Chemistry, INDUCED SYSTEMIC RESISTANCE, Experimental Organism Systems, Plant Physiology, BACTERIA, Physical Sciences, Shoot, Plant Shoots, Root Hairs, Research Article, ROOT MORPHOGENESIS, EXPRESSION, lcsh:QH426-470, Arabidopsis Thaliana, Enterobacter, Crops, Brassica, Root hair, Research and Analysis Methods, 03 medical and health sciences, Model Organisms, Biosynthesis, Stress, Physiological, Plant and Algal Models, Plant-Environment Interactions, Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, BIOSYNTHESIS, Plant Defenses, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Plant Ecology, Ecology and Environmental Sciences, Organic Chemistry, fungi, Organisms, Chemical Compounds, Biology and Life Sciences, Ethylenes, Plant Pathology, 15. Life on land, biology.organism_classification, Hormones, lcsh:Genetics, 030104 developmental biology, Chemical Properties, chemistry, Seedlings, 13. Climate action, ARABIDOPSIS-THALIANA, Potassium, Bacteria, Crop Science, 010606 plant biology & botany
Abstract: Several plant species require microbial associations for survival under different biotic and abiotic stresses. In this study, we show that Enterobacter sp. SA187, a desert plant endophytic bacterium, enhances yield of the crop plant alfalfa under field conditions as well as growth of the model plant Arabidopsis thaliana in vitro, revealing a high potential of SA187 as a biological solution for improving crop production. Studying the SA187 interaction with Arabidopsis, we uncovered a number of mechanisms related to the beneficial association of SA187 with plants. SA187 colonizes both the surface and inner tissues of Arabidopsis roots and shoots. SA187 induces salt stress tolerance by production of bacterial 2-keto-4-methylthiobutyric acid (KMBA), known to be converted into ethylene. By transcriptomic, genetic and pharmacological analyses, we show that the ethylene signaling pathway, but not plant ethylene production, is required for KMBA-induced plant salt stress tolerance. These results reveal a novel molecular communication process during the beneficial microbe-induced plant stress tolerance., Author summary Plants as sessile organisms are facing multiple stresses during their lifetime. Among them, abiotic stresses, such as salt stress, can cause severe crop yield reduction, leading to food security issues in many regions of the world. In order to respond to growing food demands, especially in the context of the global climate change and increasing world population, it then becomes urgent to develop new strategies to yield crops more tolerant to abiotic stresses. One way to overcome these challenges is to take advantage of plant beneficial microbes, defined as plant growth promoting bacteria (PGPB). In this study, we report the beneficial effect of Enterobacter sp. SA187 on plant growth under salt stress conditions. SA187 increased the yield of the forage crop alfalfa when submitted to different saline irrigations in field trials. Moreover, using the model plant Arabidopsis thaliana, we demonstrate that SA187 mediates its beneficial activity by producing 2-keto-4-methylthiobutyric acid (KMBA), which modulates the plant ethylene signaling pathway. This study highlights a novel mechanism involved in plant-PGPB interaction, and proves that endophytic bacteria can be efficiently used to enhance yield of current crops under salt stress conditions.
Published: 2018

31. Ambivalent Role of Rotamers in Cyclic(alkyl)(amino)carbene Ruthenium Complexes for Enantioselective Ring-Opening Cross-Metathesis

Author: Jennifer Morvan, François Vermersch, Ziyun Zhang, Thomas Vives, Thierry Roisnel, Christophe Crévisy, Laura Falivene, Luigi Cavallo, Nicolas Vanthuyne, Guy Bertrand, Rodolphe Jazzar, Marc Mauduit, Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), UCSD-CNRS Joint Research Chemistry Laboratory (UMI 3555), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), University of California (UC), King Abdullah University of Science and Technology (KAUST), Università degli Studi di Salerno = University of Salerno (UNISA), Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Region Bretagne (ARED 2018 'Biometa') [ANR-19-CE07-0017 ChiCAAC], Agence Nationale de la Recherche [DE-SC0009376], U.S. Department of Energy, Office of Science, Basic Energy Sciences, Catalysis Science Program, King Abdu l l a h University of Science and Technology (KAUST), 601, and ANR-19-CE07-0017,ChiCAAC,Carbènes alkyl amino cycliques chiraux en catalyse asymétrique(2019)
Subjects: Inorganic Chemistry, Organic Chemistry, [CHIM]Chemical Sciences, Physical and Theoretical Chemistry
Abstract: International audience; The development of highly efficient enantioselective olefin metathesis catalysts is a significant challenge. Using optically pure chiral cyclic (alkyl)(amino)carbene (ChiCAAC) ligands combined with preliminary mechanistic insights and density functional theory (DFT) computations, we show that catalytic performances in this field can be impaired by the formation of rotamers before the enantio-determining step. Using DFT, we also demonstrate that these results can help accelerate the process of ligand discovery by providing faster methods to discriminate potential candidates.
Published: 2023

32. TURBULENT BURNING CHARACTERISTICS OF FACE GASOLINE AND TPRF BLEND ASSOCIATED WITH THE SAME RON AT ELEVATED PRESSURES

Author: Mannaa, O., Brequigny, Pierre, Mounaïm-Rousselle, Christine, Foucher, Fabrice, Chung, S.H., W.L, Roberts, King Abdullah University of Science and Technology (KAUST), Laboratoire pluridisciplinaire de recherche en ingénierie des systèmes, mécanique et énergétique (PRISME), Université d'Orléans (UO)-Institut National des Sciences Appliquées - Centre Val de Loire (INSA CVL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Laboratoire Pluridisciplinaire de Recherche en Ingénierie des Systèmes, Mécanique et Energétique (PRISME), Université d'Orléans (UO)-Ecole Nationale Supérieure d'Ingénieurs de Bourges (ENSI Bourges), King Abdullah University of Science and Technology (KAUST) and Saudi Aramco under the FUELCOM program, and Bréquigny, Pierre
Subjects: [SPI.FLUID]Engineering Sciences [physics]/Reactive fluid environment, [SPI.FLUID] Engineering Sciences [physics]/Reactive fluid environment, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2017

33. Synthèse de nanocomposites carbone-métal multibrins par décharges dans l'heptane entre deux électrodes métalliques

Author: Hamdan, A., Kabbara, H., Courty, M.-A., Cha, M., Martinez, J.-M., Belmonte, T., Clean Combustion Research Center - CCRC (Thuwal, Saudi Arabia), King Abdullah University of Science and Technology (KAUST), Institut Jean Lamour (IJL), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Procédés, Matériaux et Energie Solaire (PROMES), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Département de Physique, Université de Montréal, Quebec, H3C 3J7, Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
Subjects: [PHYS]Physics [physics], dielectrophoresis, [SDU]Sciences of the Universe [physics], discharge in liquids, [SDE]Environmental Sciences, [SPI.PLASMA]Engineering Sciences [physics]/Plasmas, metal/carbon nanocomposite, nanoparticle synthesis, ComputingMilieux_MISCELLANEOUS, [SPI.MAT]Engineering Sciences [physics]/Materials
Abstract: International audience; We studied composite wires assembled from electric field-driven nanoparticles in a dielectric liquid (heptane) to elucidate the exact processes and controlling factors involved in the synthesis of the multi-phase nanocomposites. Filamentary wires are synthesized by a two-step process: (1) abundant nanoparticle production, mostly of car-bonaceous types, from heptane decomposition by spark discharge and of metal nanoparticles by electrode erosion and (2) assembly of hydrogenated amorphous car-bonaceous nano-clusters with incorporated metal nanoparticles forming wires by dielec-trophoretic transport while maintaining a high electric field between electrodes kept sufficiently separated to avoid breakdown. Four types of nanocomposites products are identified to form at different steps in distinctive zones of the setup. The black carbona-ceous agglomerates with metal spherules made by electrode erosion represent the pyrolytic residues of heptane decomposition by spark discharge during step 1. The filamentary wires grown in the interelectrode gap during step 2 get assembled by dielectrophoretic transport and chaining forces. Their great stability is shown to express the concurrent effect of polymerization favoured by the abundance of metal catalysts. The nature, abundance, and transformation of solid particles from the source materials versus discharge conditions control the morphological and compositional diversity of the wires. The production of mineral and metal nano-particles traces the efficiency of dielectrophoresis to separate compound particle mixtures by size and to co-synthesize nanostructured microcrystals and nanocomposites. The link between impurities and the variability from nano-to micro
Published: 2017

34. Integration of ammonia-plasma-functionalized graphene nanodiscs as charge trapping centers for nonvolatile memory applications

Author: Ching Hsiang Chen, Chao-Sung Lai, Jer-Chyi Wang, Lain-Jong Li, Mohamed Boutchich, Ching-Shiun Chen, Kai-Ping Chang, Chih-Ting Lin, Chang-Hsiao Chen, Ching Yuan Su, Fethullah Güneş, Department of Electronic Engineering, Chang Gung University, Guishan Dist., Taoyuan 33302, Taiwan, Chang Gung University, Department of Electronic Engineering, Ming Chi University of Technology, Taishan Dist., New Taipei City 24301, Taiwan, Department of Neurosurgery, Chang Gung Memorial Hospital, Guishan Dist., Taoyuan 33305, Taiwan, Department of Mechanical Engineering, National Central University, Jhongli Dist., Taoyuan 32001, Taiwan, Laboratoire Génie électrique et électronique de Paris ( GeePs ), Centre National de la Recherche Scientifique ( CNRS ) -CentraleSupélec-Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris-Sud - Paris 11 ( UP11 ), Department of Materials Science and Engineering, Izmir Kâtip Çelebi University, Cigli Main Campus, Izmir 35620, Turkey, Center for General Education, Chang Gung University, Guishan Dist., Taoyuan 33302, Taiwan, Sustainable Energy Development Center, National Taiwan University of Science and Technology, Taipei 10607, Taiwan, Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia, King Abdullah University of Science and Technology ( KAUST ), Laboratoire Génie électrique et électronique de Paris (GeePs), Université Paris-Sud - Paris 11 (UP11)-Université Pierre et Marie Curie - Paris 6 (UPMC)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Department of Automatic Control Engineering, Feng Chia University, Institute of Atomic and Molecular Sciences [Taipei] (IAMS), Academia Sinica, King Abdullah University of Science and Technology (KAUST), Department of nephrology, Department of Mechanical Engineering [Taïwan], and National Central University [Taiwan] (NCU)
Subjects: Fabrication, Materials science, [ SPI.MAT ] Engineering Sciences [physics]/Materials, Nanoparticle, Nanotechnology, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, law.invention, [SPI.MAT]Engineering Sciences [physics]/Materials, symbols.namesake, law, Etching (microfabrication), General Materials Science, Fourier transform infrared spectroscopy, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, ComputingMilieux_MISCELLANEOUS, Graphene, General Chemistry, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Non-volatile memory, symbols, Surface modification, [ SPI.NANO ] Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, 0210 nano-technology, Raman spectroscopy
Abstract: Graphene nanodiscs (GNDs), functionalized using NH3 plasma, as charge trapping sites (CTSs) for non-volatile memory applications have been investigated in this study. The fabrication process relies on the patterning of Au nanoparticles (Au-NPs), whose thicknesses are tuned to adjust the GND density and size upon etching. A GND density as high as 8 × 1011 cm−2 and a diameter of approximately 20 nm are achieved. The functionalization of GNDs by NH3 plasma creates N H+ functional groups that act as CTSs, as observed by Raman and Fourier transform infrared spectroscopy. This inherently enhances the density of CTSs in the GNDs, as a result, the memory window becomes more than 2.4 V and remains stable after 104 operating cycles. The charge loss is less than 10% for a 10-year data retention testing, making this low-temperature process suitable for low-cost non-volatile memory applications on flexible substrates.
Published: 2017

35. Flame chemiluminescence from CO2- and N2-diluted laminar CH4 /air premixed flames

Author: Daniel Durox, Thibault F. Guiberti, Thierry Schuller, Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), King Abdullah University of Science and Technology - KAUST (SAUDI ARABIA), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), CentraleSupélec (FRANCE), King Abdullah University of Science and Technology (KAUST), Laboratoire d'Énergétique Moléculaire et Macroscopique, Combustion (EM2C), Université Paris Saclay (COmUE)-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec, Clean Combustion Research Center - CCRC (Thuwal, Saudi Arabia), Institut de mécanique des fluides de Toulouse (IMFT), 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, and Institut National Polytechnique de Toulouse - INPT (FRANCE)
Subjects: Premixed flames, Chemiluminescence, Laminar flames, 020209 energy, General Chemical Engineering, Mécanique des fluides, Analytical chemistry, General Physics and Astronomy, Energy Engineering and Power Technology, Biogas, 02 engineering and technology, 7. Clean energy, Diluent, law.invention, 020401 chemical engineering, law, 0202 electrical engineering, electronic engineering, information engineering, 0204 chemical engineering, Spectrometer, Chemistry, [SPI.FLUID]Engineering Sciences [physics]/Reactive fluid environment, Laminar flow, General Chemistry, Emission intensity, Adiabatic flame temperature, Dilution, Fuel Technology, Intensity (heat transfer)
Abstract: International audience; An experimental and numerical investigation of the chemiluminescence signals from OH∗ , CH∗ , and CO2 ∗ is conducted for laminar premixed conical CH4/air flames diluted with CO2 or N2. Experiments are con- ducted either at fixed equivalence ratio or fixed adiabatic flame temperature. An ICCD camera, equipped with different narrow bandpass filters, is used to record flame images at 307 nm (OH∗), 430 nm (CH∗), and 455 nm (CO2∗). A spectrometer is also used to correct the OH∗ and CH∗ emissions from the CO2∗ broadband background emission. Measured chemiluminescence intensities are then compared to one dimensional freely-propagating-flame direct simulations accounting for the chemistry of the excited radicals. Simulations predict accurately the OH∗ chemiluminescence intensity, independently of the diluent nature and concentration. Correction for the CO2∗ background has a weak influence on the recorded OH∗ signal. Predictions of CH∗ emissions are also in good agreement with experimental data if the CO2∗ back- ground intensity is subtracted from intensity measurements. Measured and calculated CO2∗ emissions lead to acceptable results using a simplified chemistry mechanism for CO2∗ and an heuristic model for its emission intensity. Finally, it is shown that CO2 dilution modifies chemiluminescence intensity couples and particularly the OH∗/CO2∗ intensity ratio. These ratios regularly decrease with CO2 dilution, a feature which is reproduced by the simulations. It is then shown that the ratio OH∗/CO2∗ is well suited to infer the CO2 diluent concentration in diluted CH4/air flames, a method which appears not feasible for sensing N2 in N2-diluted CH4/air flames.
Published: 2017

36. Reactive surface organometallic complexes observed using dynamic nuclear polarization surface enhanced NMR spectroscopy

Author: Lyndon Emsley, Andrei Gurinov, David Gajan, Edy Abou-Hamad, Bilel Hamzaoui, Anissa Bendjeriou-Sedjerari, Eva Pump, Jean-Marie Basset, Anne Lesage, Dalaver H. Anjum, Jasmine Viger-Gravel, Manoja K. Samantaray, KAUST Catalysis Center (KCC), King Abdullah University of Sciences & Technologie, Ecole Polytechnique Fédérale de Lausanne (EPFL), Imaging & Characterizat Lab, King Abdullah University of Science and Technology (KAUST), Solid-State NMR Methods for Materials - Méthodes de RMN à l'état solide pour les matériaux, Institut des Sciences Analytiques (ISA), Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), This work received support from the King Abdullah University of Science and Technology (KAUST) and ERC Advanced Grant No. 320860, European Project: 320860,EC:FP7:ERC,ERC-2012-ADG_20120216,HI-SENS(2013), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Pore size, Nitroxide mediated radical polymerization, 010405 organic chemistry, Chemistry, Radical, fungi, technology, industry, and agriculture, Analytical chemistry, food and beverages, hemic and immune systems, chemical and pharmacologic phenomena, General Chemistry, Nuclear magnetic resonance spectroscopy, 010402 general chemistry, Photochemistry, 01 natural sciences, 0104 chemical sciences, NMR spectra database, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [CHIM]Chemical Sciences, Polarization (electrochemistry), Porous medium
Abstract: Reactive surface species immobilized inside porous materials with suitably small windows can be studied by DNP SENS., Dynamic Nuclear Polarization Surface Enhanced NMR Spectroscopy (DNP SENS) is an emerging technique that allows access to high-sensitivity NMR spectra from surfaces. However, DNP SENS usually requires the use of radicals as an exogenous source of polarization, which has so far limited applications for organometallic surface species to those that do not react with the radicals. Here we show that reactive surface species can be studied if they are immobilized inside porous materials with suitably small windows, and if bulky nitroxide bi-radicals (here TEKPol) are used as the polarization source and which cannot enter the pores. The method is demonstrated by obtaining significant DNP enhancements from highly reactive complelxes [( 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 Si–O–)W(Me)5] supported on MCM-41, and effects of pore size (6.0, 3.0 and 2.5 nm) on the performance are discussed.
Published: 2017

37. Horizontal acquisition of Symbiodiniaceae in the Anemonia viridis (Cnidaria, Anthozoa) species complex

Author: Didier Forcioli, Cédric Mallien, Paola Furla, Barbara Porro, Eric Röttinger, Benjamin C. C. Hume, Thamilla Zamoum, Christian R. Voolstra, Université Côte d’Azur, CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), 28 avenue de Valombrose, 06107 Nice, France, Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), King Abdullah University of Science and Technology (KAUST), Department of Biology, University of Konstanz, Konstanz, Germany, Université Nice Sophia Antipolis (1965 - 2019) (UNS), and Röttinger, Eric
Subjects: 0106 biological sciences, 0301 basic medicine, Species complex, [SDV]Life Sciences [q-bio], Sea anemone, 010603 evolutionary biology, 01 natural sciences, Anemonia, 03 medical and health sciences, Anthozoa, ddc:570, Mediterranean Sea, Genetics, Animals, 14. Life underwater, Symbiosis, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Phenotypic plasticity, biology, Anemone, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, [SDV] Life Sciences [q-bio], Holobiont, Sea Anemones, 030104 developmental biology, Evolutionary biology, Dinoflagellida, Adaptation
Abstract: [poster presented at iMarCo congress, abstract from the Molecular Ecology related article] All metazoans are in fact holobionts, resulting from the association of several organisms, and organismal adaptation is then due to the composite response of this association to the environment. Deciphering the mechanisms of symbiont acquisition in a holobiont is therefore essential to understanding the extent of its adaptive capacities. In cnidarians, some species acquire their photosynthetic symbionts directly from their parents (vertical transmission) but may also acquire symbionts from the environment (horizontal acquisition) at the adult stage. The Mediterranean snakelocks sea anemone, Anemonia viridis (Forskål, 1775), passes down symbionts from one generation to the next by vertical transmission, but the capacity for such horizontal acquisition is still unexplored. To unravel the flexibility of the association between the different host lineages identified in A.viridis and its Symbiodiniaceae, we genotyped both the animal hosts and their symbiont communities in members of host clones in five different locations in the North Western Mediterranean Sea. The composition of within-host–symbiont populations was more dependent on the geographical origin of the hosts than their membership to a given lineage or even to a given clone. Additionally, similarities in host–symbiont communities were greater among genets (i.e. among different clones) than among ramets (i.e. among members of the same given clonal genotype). Taken together, our results demonstrate that A.viridis may form associations with a range of symbiotic dinoflagellates and suggest a capacity for horizontal acquisition. A mixed-mode transmission strategy in A.viridis, as we posit here, may help explain the large phenotypic plasticity that characterizes this anemone.
Published: 2023
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38. Selective Metathesis of α-Olefins from Bio-Sourced Fischer–Tropsch Feeds

Author: Albert Poater, Mikael Berthod, Etienne Borré, Helene Olivier-Bourbigou, Olivier Baslé, Pierre Queval, Mathieu Rouen, Luigi Cavallo, Marc Mauduit, Francois Hugues, Laura Falivene, Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), King Abdullah University of Science and Technology (KAUST), Dept Quim, Universitat de Girona (UdG), IFP Energies nouvelles (IFPEN), This work was supported by the European Community through the seventh framework program (CP-FP 211468-2 EUMET, grant to M.R., L.F., and E.B.). M.M. thanks the CNRS, the ENSCR, Rennes Métropole, and the Région-Bretagne for their financial support. A.P. thanks the Spanish MINECO for project CTQ2014-59832-JIN, and L.C. acknowledges funding from the King Abdullah University of Science and Technology (KAUST)., Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Ministerio de Economía y Competitividad (Espanya)
Subjects: DECOMPOSITION, Isomerization, Metathesis (Chemistry), Fischer-Tropsch process, olefin metathesis, ruthenium, unsymmetrical NRC, Fischer-Tropsch feeds, isomerization, selectivity, N-HETEROCYCLIC CARBENE, GRUBBS CATALYSTS, NEW-GENERATION, ISOMERIZATION, COMPLEXES, EFFICIENT, LIGANDS, ALCOHOLS, STABILITY, Fischer-Tropsch, Procés, chemistry.chemical_element, Fraction (chemistry), Alkenes, 010402 general chemistry, Metathesis, 01 natural sciences, 7. Clean energy, Catalysis, unsymmetrical NHC, Metàtesi (Química), Organic chemistry, [CHIM]Chemical Sciences, Naphtha, 010405 organic chemistry, Fischer–Tropsch process, General Chemistry, Fischer−Tropsch feeds, 0104 chemical sciences, Ruthenium, chemistry, Alquens, Selectivity, Isomerització
Abstract: The search for a low-cost process for the valorization of linear α-olefins combining high productivity and high selectivity is a longstanding goal for chemists. Herein, we report a soluble ruthenium olefin metathesis catalyst that performs the conversion of linear α-olefins to longer internal linear olefins with high selectivity (>99%) under neat conditions at low loadings (50 ppm) and without the need of expensive additives. This robust catalytic process allowed us to efficiently and selectively re-equilibrate the naphtha fraction (C5–C8) of a Fischer–Tropsch feed derived from non-petroleum resources to a higher-value product range (C9–C14), useful as detergent and plasticizer precursors This work was supported by the European Community through the seventh framework program (CP-FP 211468-2 EUMET, grant to M.R., L.F., and E.B.). M.M. thanks the CNRS, the ENSCR, Rennes Métropole, and the Région-Bretagne for their financial support. A.P. thanks the Spanish MINECO for project CTQ2014- 59832-JIN, and L.C. acknowledges funding from the King Abdullah University of Science and Technology (KAUST)
Published: 2016

39. Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor

Author: Christophe Sola, Elif Aktaş, Michel K. Gomgnimbou, Füsun Cömert, Francesc Coll, Arnab Pain, Stefan Panaiotov, Hiromi Ano, Guislaine Refrégier, Ruth McNerney, Taane G. Clark, Tomoshige Matsumoto, Izuo Tsuyuguchi, Tetsuya Takashima, Edgar Abadia, Jody Phelan, Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Instituto Venezolano de Investigaciones Cientificas ( IVIC ), Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Şişli Etfal Research and Training Hopital, Faculty of Medicine, Bülent Ecevit University, Zonguldak, National Center of Parasitic and Infectious Diseases, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine ( LSHTM ), Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, King Abdullah University of Science and Technology ( KAUST ), 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), Instituto Venezolano de Investigaciones Cientificas (IVIC), London School of Hygiene and Tropical Medicine (LSHTM), King Abdullah University of Science and Technology (KAUST), and Zonguldak Bülent Ecevit Üniversitesi
Subjects: DNA, Bacterial, 0301 basic medicine, Microbiology (medical), Most recent common ancestor, Genotype, Turkey, [SDV]Life Sciences [q-bio], Locus (genetics), Minisatellite Repeats, Biology, History, 18th Century, Pathogen evolution, Polymorphism, Single Nucleotide, Microbiology, Genome, Evolution, Molecular, History, 17th Century, 03 medical and health sciences, Monophyly, Japan, Phylogenetics, Genetics, Humans, Tuberculosis, Epidemics, Molecular clock, Molecular Biology, History, Ancient, Phylogeny, Ecology, Evolution, Behavior and Systematics, Ancestor, Molecular Epidemiology, [ SDV ] Life Sciences [q-bio], Mycobacterium tuberculosis, History, Medieval, 3. Good health, Molecular Typing, Genetic divergence, Phylogeography, 030104 developmental biology, Infectious Diseases, History, 16th Century
Abstract: Two geographically distant M. tuberculosis sublineages, Tur from Turkey and T3-Osaka from Japan, exhibit partially identical genotypic signatures (identical 12-loci MIRU-VNTR profiles, distinct spoligotyping patterns). We investigated T3-Osaka and Tur sublineages characteristics and potential genetic relatedness, first using MIRU-VNTR locus analysis on 21 and 25 samples of each sublineage respectively, and second comparing Whole Genome Sequences of 8 new samples to public data from 45 samples uncovering human tuberculosis diversity. We then tried to date their Most Recent Common Ancestor (MRCA) using three calibrations of SNP accumulation rate (long-term = 0.03 SNP/genome/year, derived from a tuberculosis ancestor of around 70,000 years old; intermediate = 0.2 SNP/genome/year derived from a Peruvian mummy; short-term = 0.5 SNP/genome/year). To disentangle between these scenarios, we confronted the corresponding divergence times with major human history events and knowledge on human genetic divergence. We identified relatively high intrasublineage diversity for both T3-Osaka and Tur. We definitively proved their monophyly; the corresponding super-sublineage (referred to as “T3-Osa-Tur”) shares a common ancestor with T3-Ethiopia and Ural sublineages but is only remotely related to other Euro-American sublineages such as X, LAM, Haarlem and S. The evolutionary scenario based on long-term evolution rate being valid until T3-Osa-Tur MRCA was not supported by Japanese fossil data. The evolutionary scenario relying on short-term evolution rate since T3-Osa-Tur MRCA was contradicted by human history and potential traces of past epidemics. T3-Osaka and Tur sublineages were found likely to have diverged between 800 y and 2000 years ago, potentially at the time of Mongol Empire. Altogether, this study definitively proves a strong genetic link between Turkish and Japanese tuberculosis. It provides a first hypothesis for calibrating TB Euro-American lineage molecular clock; additional studies are needed to reliably date events corresponding to intermediate depths in tuberculosis phylogeny. © 2016 Elsevier B.V., Research Councils UK King Abdullah University of Science and Technology, This study was financed by UMR9198, CEA-CNRS-UPS, Institut de Biologie Intégrative de la Cellule, Gif-sur-Yvette, France . GR and CS hold respectively an assistant professorship and a full professorship position at University Paris-Sud. No competitive interest is to be declared. JP is supported by a BBSRC UK PhD studentship. TGC is funded by the Medical Research Council UK (Grant no. MR/K000551/1 , MR/M01360X/1 , MR/N010469/1 )., This work was initiated in 2005 in the Institut Pasteur of Guadeloupe, and Dr. Nalin Rastogi and Dr. Riza Durmaz are acknowledged for material support, stimulating discussions, and/or for having initiated long-term collaborative studies on MTBC DNA from Turkey. During the 2007–2008 period, T. Dos Vultos, J. Rauzier and B. Gicquel through the extensive 3R MTBC gene diversity study, provided an important advance to the T3-Osa-Tur hypothesis by providing confirmatory preliminary results. Technical support was provided by the Luminex Corp. (Austin, TX) for SNP genotyping, and by King Abdullah University of Science and Technology (KAUST) for Whole Genome Sequencing. GR and CS acknowledge recurrent support from CNRS-Univ. Paris-Sud.
Published: 2016

40. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Author: Eichiro Ichiishi, Dmitri Beglov, Bernard Maigret, Gyu Rie Lee, Artem B. Mamonov, Shoshana J. Wodak, Jonathan C. Fuller, Dima Kozakov, Jong Young Joung, Petr Popov, Xiaofeng Yu, Keehyoung Joo, João P. G. L. M. Rodrigues, Anna Vangone, Koen M. Visscher, Xiaoqin Zou, Paul A. Bates, Andriy Kryshtafovych, Shourya S. Roy Burman, Daisuke Kihara, Romina Oliva, Efrat Ben-Zeev, Jeffrey J. Gray, Yang Shen, Li C. Xue, Sameer Velankar, Emilie Neveu, Shruthi Viswanath, Dina Schneidman-Duhovny, Juan Esquivel-Rodríguez, Mieczyslaw Torchala, Amit Roy, Alexandre M. J. J. Bonvin, David R. Hall, Tanggis Bohnuud, Xusi Han, David W. Ritchie, Ron Elber, Daisuke Kuroda, Zhiwei Ma, Joan Segura, Carlos A. Del Carpio, Nicholas A. Marze, Jong Yun Kim, Andrej Sali, Petras J. Kundrotas, Ezgi Karaca, Neil J. Bruce, Chaok Seok, Panagiotis L. Kastritis, Shen You Huang, Ilya A. Vakser, Lim Heo, Sanbo Qin, Raphael A. G. Chaleil, Adrien S. J. Melquiond, Miguel Romero-Durana, Anisah W. Ghoorah, Surendra S. Negi, Andrey Tovchigrechko, Françoise Ochsenbein, Narcis Fernandez-Fuentes, Liming Qiu, Miriam Eisenstein, Mehdi Nellen, Marie-Dominique Devignes, Lenna X. Peterson, Jinchao Yu, Minkyung Baek, Brian G. Pierce, Hasup Lee, Toshiyuki Oda, Rebecca C. Wade, Raphael Guerois, Juan Fernández-Recio, Iain H. Moal, Edrisse Chermak, Sergei Grudinin, Sangwoo Park, Ivan Anishchenko, Chengfei Yan, Thom Vreven, Kentaro Tomii, Bing Xia, Hyung Rae Kim, Chiara Pallara, Jooyoung Lee, Kazunori D. Yamada, Xianjin Xu, Kenichiro Imai, Zhiping Weng, Luigi Cavallo, Tyler M. Borrman, Jianlin Cheng, Marc F. Lensink, Huan-Xiang Zhou, Jilong Li, Gydo C. P. van Zundert, Brian Jiménez-García, Tsukasa Nakamura, Scott E. Mottarella, Sandor Vajda, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] ( IRI ), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique ( CNRS ), European Molecular Biology Laboratory, European Bioinformatics Institute, Genome Center [UC Davis], University of California at Davis, Research Support Computing [Columbia], University of Missouri-Columbia, Bioinformatics Consortium and Department of Computer Science [Columbia], Department of Bioengineering and Therapeutic Sciences, University of California [San Francisco] ( UCSF ), Department of Pharmaceutical Chemistry, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, University of California [San Francisco] ( UCSF ) -California Institute for Quantitative Biosciences, GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, Centro Nacional de Biotecnología (CSIC), Institute of Biological, Environmental and Rural Sciences ( IBERS ), Institute for Computational Engineering and Sciences [Austin] ( ICES ), University of Texas at Austin [Austin], Department of Computer Science, Department of Chemistry, Algorithms for Modeling and Simulation of Nanosystems ( NANO-D ), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Laboratoire Jean Kuntzmann ( LJK ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Institut Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ) -Institut National Polytechnique de Grenoble ( INPG ), Moscow Institute of Physics and Technology [Moscow] ( MIPT ), Seoul National University [Seoul], Florida State University [Tallahassee] ( FSU ), Computational Algorithms for Protein Structures and Interactions ( CAPSID ), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Department of Complex Systems, Artificial Intelligence & Robotics ( LORIA - AIS ), Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Laboratoire Lorrain de Recherche en Informatique et ses Applications ( LORIA ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ), University of Mauritius, Biomolecular Modelling Laboratory, The Francis Crick Institute, Lincoln's Inn Fields Laboratory, G-INCPM, Weizmann Institute of Science, Chemical Research Support [Rehovot], Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch ( UTMB ), Program in Bioinformatics and Integrative Biology [Worcester], University of Massachusetts Medical School [Worcester] ( UMASS ), 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 ), Bijvoet Center for Biomolecular Research [Utrecht], Utrecht University [Utrecht], Dalton Cardiovascular Research Center [Columbia], Department of Computer Science [Columbia], Informatics Intitute, Department of Biochemistry, University of Missouri, UNIVERSITY OF MISSOURI, Toyota Technological Institute at Chicago [Chicago] ( TTIC ), Department of Biological Sciences, Purdue University, Purdue University [West Lafayette], Department of Computer Science [Purdue], Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, Molecular and Cellular Modeling Group, Heidelberg Institute of Theoretical Studies, Center for Molecular Biology ( ZMBH ), Universität Heidelberg [Heidelberg], Interdisciplinary Center for Scientiﬁc Computing ( IWR ), Department of Molecular Biosciences [Lawrence], University of Kansas [Lawrence] ( KU ), Computational Biology Research Center ( CBRC ), National Institute of Advanced Industrial Science and Technology ( AIST ), Graduate School of Frontier Sciences, The University of Tokyo, Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center - Centro Nacional de Supercomputacion ( BSC - CNS ), Center for In-Silico Protein Science, Korea Institute for Advanced Study ( KIAS ), Center for Advanced Computation, Department of Biomedical Engineering [Boston], Boston University [Boston] ( BU ), Institute of Biological Diversity, International Pacific Institute of Indiana, Drosophila Genetic Resource Center, Kyoto Institute of Technology, International University of Health and Welfare Hospital ( IUHW Hospital ), International University of Health and Welfare Hospital, Department of Chemical and Biomolecular Engineering [Baltimore], Johns Hopkins University ( JHU ), Program in Molecular Biophysics [Baltimore], King Abdullah University of Science and Technology ( KAUST ), University of Naples, J Craig Venter Institute, Structural Biology Research Center, VIB, 1050 Brussels, Belgium, Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq] (IRI), Université de Lille, Sciences et Technologies-Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), University of Missouri [Columbia] (Mizzou), University of Missouri System, University of California [San Francisco] (UC San Francisco), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Biological, Environmental and Rural Sciences (IBERS), Institute for Computational Engineering and Sciences [Austin] (ICES), Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Moscow Institute of Physics and Technology [Moscow] (MIPT), Seoul National University [Seoul] (SNU), Florida State University [Tallahassee] (FSU), Computational Algorithms for Protein Structures and Interactions (CAPSID), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Complex Systems, Artificial Intelligence & Robotics (LORIA - AIS), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Biomolecular Modelling Laboratory [London], The Francis Crick Institute [London], Weizmann Institute of Science [Rehovot, Israël], The University of Texas Medical Branch (UTMB), University of Massachusetts Medical School [Worcester] (UMASS), University of Massachusetts System (UMASS)-University of Massachusetts System (UMASS), 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), Assemblage moléculaire et intégrité du génome (AMIG), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-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)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), University of Missouri System-University of Missouri System, Toyota Technological Institute at Chicago [Chicago] (TTIC), Department of Biological Sciences [Lafayette IN], Heidelberg Institute for Theoretical Studies (HITS ), Center for Molecular Biology (ZMBH), Universität Heidelberg [Heidelberg] = Heidelberg University, Interdisciplinary Center for Scientiﬁc Computing (IWR), University of Kansas [Lawrence] (KU), Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), The University of Tokyo (UTokyo), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Korea Institute for Advanced Study (KIAS), Boston University [Boston] (BU), International University of Health and Welfare Hospital (IUHW Hospital), Johns Hopkins University (JHU), King Abdullah University of Science and Technology (KAUST), University of Naples Federico II = Università degli studi di Napoli Federico II, J. Craig Venter Institute, VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Droit et Santé-Université de Lille, Sciences et Technologies, University of California-University of California, University of California [San Francisco] (UCSF), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), University of Naples Federico II, Barcelona Supercomputing Center, NMR Spectroscopy, and Sub NMR Spectroscopy
Subjects: 0301 basic medicine, Protein Conformation, alpha-Helical, Protein Folding, Computer science, International Cooperation, Amino Acid Motifs, Oligomer state, Homoprotein, DATA-BANK, computer.software_genre, Molecular Docking Simulation, Biochemistry, CAPRI Round 30, DESIGN, Structural Biology, ALIGN, Blind prediction, AFFINITY, Protein interaction, Enginyeria biomèdica [Àrees temàtiques de la UPC], ZDOCK, Oligomer State, computer.file_format, Articles, Protein structure prediction, Proteïnes--Investigació, 3. Good health, WEB SERVER, CASP, Thermodynamics, Data mining, CAPRI, Protein docking, Molecular Biology, Algorithms, INTERFACES, Protein Binding, [ INFO.INFO-MO ] Computer Science [cs]/Modeling and Simulation, Bioinformatics, STRUCTURAL BIOLOGY, Computational biology, Molecular Dynamics Simulation, Article, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Heteroprotein, Humans, Protein binding, Macromolecular docking, Protein Interaction Domains and Motifs, Homology modeling, ALGORITHM, Protein-protein docking, Internet, Binding Sites, Models, Statistical, 030102 biochemistry & molecular biology, Bacteria, Sequence Homology, Amino Acid, Computational Biology, Proteins, Protein Data Bank, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Protein Structure, Tertiary, 030104 developmental biology, Structural biology, Docking (molecular), Protein structure, Protein Conformation, beta-Strand, Protein Multimerization, oligomer state, blind prediction, protein interaction, protein docking, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Software
Abstract: We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein–protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. We are most grateful to the PDBe at the European Bioinformatics Institute in Hinxton, UK, for hosting the CAPRI website. Our deepest thanks go to all the structural biologists and to the following structural genomics initiatives: Northeast Structural Genomics Consortium, Joint Center for Structural Genomics, NatPro PSI:Biology, New York Structural Genomics Research Center, Midwest Center for Structural Genomics, Structural Genomics Consortium, for contributing the targets for this joint CASP-CAPRI experiment. MFL acknowledges support from the FRABio FR3688 Research Federation “Structural & Functional Biochemistry of Biomolecular Assemblies.”
Published: 2016

41. The structure and binding mode of citrate in the stabilization of gold nanoparticles

Author: Lyndon Emsley, Hind Al-Johani, Luigi Cavallo, Abdesslem Jedidi, Michael J. Kelly, Jean-Marie Basset, David Gajan, Andrei Gurinov, Samy Ould-Chikh, Mohamed N. Hedhili, Jasmine Viger-Gravel, Shiv Shankar Sangaru, Edy Abou-Hamad, Cory M. Widdifield, Dalaver H. Anjum, Mohamad El Eter, KAUST Catalysis Center (KCC), King Abdullah University of Sciences & Technologie, Chem Dept, University of Tabuk, Dept Chem, King Abdulaziz University, Department of Chemistry, Durham University, Institut des sciences et ingénierie chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Solid-State NMR Methods for Materials - Méthodes de RMN à l'état solide pour les matériaux, Institut des Sciences Analytiques (ISA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Imaging & Characterizat Lab, King Abdullah University of Science and Technology (KAUST), This work received support from the King Abdullah University of Science and Technology (KAUST) and ERC Advanced Grant No. 320860., European Project: 320860,EC:FP7:ERC,ERC-2012-ADG_20120216,HI-SENS(2013), Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)
Subjects: MECHANISM, ADSORPTION, Denticity, SURFACE, Trace Amounts, General Chemical Engineering, 02 engineering and technology, METAL NANOPARTICLES, 010402 general chemistry, 01 natural sciences, ANIONS, law.invention, Ion, chemistry.chemical_compound, Oxidation state, law, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Carboxylate, AU(111), Chemistry, THIN-FILM ELECTRODES, AU NANOPARTICLES, SINGLE-CRYSTAL, MICROSCOPY, General Chemistry, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Crystallography, Solid-state nuclear magnetic resonance, Colloidal gold, Electron microscope, 0210 nano-technology
Abstract: For computer time, this research used the resources of the Supercomputing Laboratory at King Abdullah University of Science & Technology (KAUST) in Thuwal, Saudi Arabia.; International audience; Elucidating the binding mode of carboxylate-containing ligands to gold nanoparticles (AuNPs) is crucial to understand their stabilizing role. A detailed picture of the three-dimensional structure and coordination modes of citrate, acetate, succinate and glutarate to AuNPs is obtained by C-13 and Na-23 solid-state NMR in combination with computational modelling and electron microscopy. The binding between the carboxylates and the AuNP surface is found to occur in three different modes. These three modes are simultaneously present at low citrate to gold ratios, while a monocarboxylate monodentate (1 kappa O-1) mode is favoured at high citrate: gold ratios. The surface AuNP atoms are found to be predominantly in the zero oxidation state after citrate coordination, although trace amounts of Au delta+ are observed. Na-23 NMR experiments show that Na+ ions are present near the gold surface, indicating that carboxylate binding occurs as a 2e(-) L-type interaction for each oxygen atom involved. This approach has broad potential to probe the binding of a variety of ligands to metal nanoparticles.
Published: 2016

42. Bacterial Rhizosphere Biodiversity from Several Pioneer Desert Sand Plants Near Jizan, Saudi Arabia

Author: Heribert Hirt, Jorge R. Osman, Michael S. DuBow, Ton Bisseling, Axel de Zélicourt, René Geurts, 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), Chemisch Biologisch Laboratorium Bodem, Wageningen University and Research [Wageningen] (WUR), Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), 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 ), Wageningen University and Research Centre [Wageningen] ( WUR ), and King Abdullah University of Science and Technology ( KAUST )
Subjects: Firmicutes, Biodiversity, [ SDE ] Environmental Sciences, 03 medical and health sciences, 16S rDNA, Botany, Laboratorium voor Moleculaire Biologie, Life Science, 030304 developmental biology, desert sand microbiome, 0303 health sciences, Rhizosphere, Pioneer species, biology, Ecology, 04 agricultural and veterinary sciences, Vegetation, 15. Life on land, biology.organism_classification, Arid, pyrosequencing, Microbial population biology, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Laboratory of Molecular Biology, Bacterial community, Proteobacteria, rhizosphere
Abstract: International audience; Life in arid regions and, in particular, hot deserts is often limited due to their harsh environmental conditions, such as large temperature fluctuations and low amounts of water. These extreme environments can influence the microbial community present on the surface sands and any rhizosphere members surrounding desert plant roots. The Jizan desert area, located in Saudi Arabia, supports particular vegetation that grows in the large sandy flat terrain. We examined five different samples, four from the rhizosphere of pioneer plants plus a surface sand sample, and used pyrosequencing of PCR-amplified V1-V3 regions of 16S rDNA genes from total extracted DNA to reveal and compare the bacterial population diversity of the samples. The results showed a total of 3,530 OTUs in the five samples, calculated using ≥ 97% sequence similarity levels. The Chao1 estimation of the bacterial diversity fluctuated from 637 to 2,026 OTUs for a given sample. The most abundant members found in the samples belong to the Bacteroidetes, Firmicutes and Proteobacteria phyla. This work shows that the Jizan desert area of Saudi Arabia can contain a diverse bacterial community on the sand and surrounding the roots of pioneer desert plants. It also shows that desert sand microbiomes can vary depending on conditions, with broad implications for sandstone monument bacterial communities
Published: 2016

43. Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes

Author: Hans-Peter Klenk, Karima Hezbri, Abdellatif Boudabous, Jean Armengaud, Arnab Sen, Petar Pujic, Faten Ghodhbane-Gtari, Maher Gtari, Philippe Normand, Louis S. Tisa, Daniele Daffonchio, Haïtham Sghaier, National Institute for Nuclear Science and Technology, Institut Supérieur de Biotechnologie de Sidi Thabet (ISBST), Laboratory Microorganismes and Biomolecular Activ, Université Tunis El Manar (UTM), Université de Carthage - University of Carthage, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Department of Botany, National University of Ireland [Galway] (NUI Galway), Biology and Environment Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Department of Food Environmental and Nutritional Sciences, (DeFENS), University of Milan, Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire (UNH), School Biology, Newcastle University, EU project BIODESERT (European Community's Seventh Framework Programme CSA-SA REGPOT-2) 245746, Université de la Manouba [Tunisie] (UMA)-Université de la Manouba [Tunisie] (UMA), Université de Tunis El Manar (UTM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Institut Supérieur de Biotechnologie de Sidi Thabet ( ISBST ), Université Tunis El-Manar, Université de Carthage, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), National University of Ireland [Galway] ( NUI Galway ), King Abdullah University of Science and Technology ( KAUST ), Department of Molecular Cellular and Biomedical Science, and University of New Hampshire ( UNH )
Subjects: 0301 basic medicine, Proteomics, Geologic Sediments, [SDV]Life Sciences [q-bio], 030106 microbiology, Biology, Microbiology, Genome, Mass Spectrometry, Actinobacteria, 03 medical and health sciences, Microbial ecology, sable, Actinomycetales, genome, Ecology, Evolution, Behavior and Systematics, Geodermatophilaceae, Genetics, [ SDV ] Life Sciences [q-bio], sahara, Biodiversity, biology.organism_classification, Adaptation, Physiological, Environmental biotechnology, Evolutionary biology, silica, Proteome, biomarker, Original Article, Adaptation, escherichia coli, biomarqueur, Chromatography, Liquid
Abstract: The Geodermatophilaceae are unique model systems to study the ability to thrive on or within stones and their proteogenomes (referring to the whole protein arsenal encoded by the genome) could provide important insight into their adaptation mechanisms. Here we report the detailed comparative genome analysis of Blastococcus saxobsidens (Bs), Modestobacter marinus (Mm) and Geodermatophilus obscurus (Go) isolated respectively from the interior and the surface of calcarenite stones and from desert sandy soils. The genome-scale analysis of Bs, Mm and Go illustrates how adaptation to these niches can be achieved through various strategies including ` molecular tinkering/ opportunism' as shown by the high proportion of lost, duplicated or horizontally transferred genes and ORFans. Using high-throughput discovery proteomics, the three proteomes under unstressed conditions were analyzed, highlighting the most abundant biomarkers and the main protein factors. Proteomic data corroborated previously demonstrated stone-related ecological distribution. For instance, these data showed starvation-inducible, biofilm-related and DNA-protection proteins as signatures of the microbes associated with the interior, surface and outside of stones, respectively.
Published: 2016

44. The role of MAPK modules and ABA during abiotic stress signaling

Author: Jean Colcombet, Axel de Zélicourt, Heribert Hirt, King Abdullah University of Science and Technology (KAUST), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA) Centre National de Recherche Scientifique (CNRS) Universite Evry Val d'Essonne (UEVE) King Abdullah University of Science and Technology (KAUST), and Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 0301 basic medicine, MAPK/ERK pathway, signaling pathway, abiotic stress, [SDV]Life Sciences [q-bio], stomata, Context (language use), Plant Science, Biology, 01 natural sciences, abscisic acid, 03 medical and health sciences, chemistry.chemical_compound, Plant Growth Regulators, Gene Expression Regulation, Plant, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Abscisic acid, Regulation of gene expression, Abiotic component, Abiotic stress, mitogen activated protein kinase, organic chemicals, fungi, food and beverages, Cell biology, 030104 developmental biology, chemistry, Biochemistry, Mitogen-activated protein kinase, Plant Stomata, biology.protein, Mitogen-Activated Protein Kinases, Signal transduction, Signal Transduction, 010606 plant biology & botany
Abstract: International audience; To respond to abiotic stresses, plants have developed specific mechanisms that allow them to rapidly perceive and respond to environmental changes. The phytohormone abscisic acid (ABA) was shown to be a pivotal regulator of abiotic stress responses in plants, triggering major changes in plant physiology. The ABA core signaling pathway largely relies on the activation of SnRK2 kinases to mediate several rapid responses, including gene regulation, stomatal closure, and plant growth modulation. Mitogen-activated protein kinases (MAPKs) have also been implicated in ABA signaling, but an entire ABA-activated MAPK module was uncovered only recently. In this review, we discuss the evidence for a role of MAPK modules in the context of different plant ABA signaling pathways.
Published: 2016

45. PtII−N-Heterocyclic Carbene Complexes in Solvent-Free Alkene Hydrosilylation

Author: Maliszewski, Benon P., Bayrakdar, Tahani A. C. A., Lambert, Perrine, Hamdouna, Lama, Trivelli, Xavier, Cavallo, Luigi, Poater, Albert, Beliš, Marek, Lafon, Olivier, van Hecke, Kristof, Ormerod, Dominic, Cazin, Catherine S. J., Nahra, Fady, Nolan, Steven P., Universiteit Gent = Ghent University (UGENT), Flemish Institute for Technological Research (VITO), Unité de Catalyse et Chimie du Solide - UMR 8181 (UCCS), Université d'Artois (UA)-Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Sciences et Technologies, King Abdullah University of Science and Technology (KAUST), Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona (IQCC), and Universitat de Girona (UdG)
Subjects: solvent-free catalysis, alkenes, hydrosilylation, N-heterocyclic carbenes, platinum, [CHIM.INOR]Chemical Sciences/Inorganic chemistry
Abstract: International audience; Herein, we report the catalytic activity of a series of platinum(II) pre-catalysts, bearing N-heterocyclic carbene (NHC) ligands, in the alkene hydrosilylation reaction. Their structural and electronic properties are fully investigated using X-ray diffraction analysis and nuclear magnetic resonance spectroscopy (NMR). Next, our study presents a structure-activity relationship within this group of pre-catalysts and gives mechanistic insights into the catalyst activation step. An exceptional catalytic performance of one of the complexes is observed, reaching a turnover number (TON) of 970 000 and a turnover frequency (TOF) of 40 417 h−1 at 1 ppm catalyst loading. Finally, an attractive solvent-free and open-to-air alkene hydrosilylation protocol, featuring efficient platinum removal (reduction of residual Pt from 582 ppm to 5.8 ppm), is disclosed.
Published: 2023

46. Assessing Phonon Coherence Using Spectroscopy

Author: Zhongwei Zhang, Yangyu Guo, Marc Bescond, Masahiro Nomura, Sebastian Volz, Jie Chen, King Abdullah University of Science and Technology (KAUST), Institut Lumière Matière [Villeurbanne] (ILM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratory for Integrated Micro Mechatronics Systems (LIMMS), The University of Tokyo (UTokyo)-Centre National de la Recherche Scientifique (CNRS), 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), The University of Tokyo (UTokyo), Institute of Industrial Science (IIS), Rockefeller University [New York], and Shanghai Jiaotong University
Subjects: [PHYS]Physics [physics], Condensed Matter::Materials Science, Condensed Matter::Superconductivity, FOS: Physical sciences, Physics - Applied Physics, Applied Physics (physics.app-ph)
Abstract: As a fundamental physical quantity of thermal phonons, temporal coherence participates in a broad range of thermal and phononic processes, while a clear methodology for the measurement of phonon coherence is still lacking. In this Lettter, we derive a theoretical model for the experimental exploration of phonon coherence based on spectroscopy, which is then validated by comparison with Brillouin light scattering data and direct molecular dynamic simulations of confined modes in nanostructures. The proposed model highlights that confined modes exhibit a pronounced wavelike behavior characterized by a higher ratio of coherence time to lifetime. The dependence of phonon coherence on system size is also demonstrated from spectroscopy data. The proposed theory allows for reassessing data of conventional spectroscopy to yield coherence times, which are essential for the understanding and the estimation of phonon characteristics and heat transport in solids in general., Comment: 4 pages, 3 figures
Published: 2023

47. A manipulation of carotenoid metabolism influence biomass partitioning and fitness in tomato

Author: Jianing Mi, Jose G. Vallarino, Ivan Petřík, Ondřej Novák, Sandra M. Correa, Monika Chodasiewicz, Michel Havaux, Manuel Rodriguez-Concepcion, Salim Al-Babili, Alisdair R. Fernie, Aleksandra Skirycz, Juan C. Moreno, King Abdullah University of Science and Technology (KAUST), Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Max-Planck-Gesellschaft, Laboratory of Growth Regulators [Univ Palacký] (LGR), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Plant Environmental Physiology and Stress Signaling (PEPSS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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), Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), and Instituto de Biología Molecular y Celular de Plantas
Subjects: Abiotic stress tolerance, [SDV]Life Sciences [q-bio], fungi, Biomass and yield, food and beverages, Bioengineering, Metabolites and lipids, Carotenoids, Applied Microbiology and Biotechnology, Biosynthetic Pathways, Solanum lycopersicum, Stress, Physiological, Apocarotenoids, Metabolic engineering, Phytohormones, Biomass, Biotechnology
Abstract: Improving yield, nutritional value and tolerance to abiotic stress are major targets of current breeding and biotechnological approaches that aim at increasing crop production and ensuring food security. Metabolic engineering of carotenoids, the precursor of vitamin-A and plant hormones that regulate plant growth and response to adverse growth conditions, has been mainly focusing on provitamin A biofortification or the production of high-value carotenoids. Here, we show that the introduction of a single gene of the carotenoid biosynthetic pathway in different tomato cultivars induced profound metabolic alterations in carotenoid, apocarotenoid and phytohormones pathways. Alterations in isoprenoid- (abscisic acid, gibberellins, cytokinins) and non-isoprenoid (auxin and jasmonic acid) derived hormones together with enhanced xanthophyll content influenced biomass partitioning and abiotic stress tolerance (high light, salt, and drought), and it caused an up to 77% fruit yield increase and enhanced fruit's provitamin A content. In addition, metabolic and hormonal changes led to accumulation of key primary metabolites (e.g. osmoprotectants and antiaging agents) contributing with enhanced abiotic stress tolerance and fruit shelf life. Our findings pave the way for developing a new generation of crops that combine high productivity and increased nutritional value with the capability to cope with climate change-related environmental challenges.
Published: 2022

48. A structural homologue of the plant receptor D14 mediates responses to strigolactones in the fungal phytopathogen Cryphonectria parasitica

Author: Valentina Fiorilli, Marco Forgia, Alexandre Saint Germain, Giulia D’Arrigo, David Cornu, Philippe Le Bris, Salim Al‐Babili, Francesca Cardinale, Cristina Prandi, Francesca Spyrakis, François‐Didier Boyer, Massimo Turina, Luisa Lanfranco, Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli studi di Torino = University of Turin (UNITO), CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] (IPSP), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), King Abdullah University of Science and Technology (KAUST), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), CRG2017/King Abdullah University of Science and TechnologyEuropean CommissionUniversità degli Studi di Torinoshort-term mobility COST fellowship (COST Action)FA 1206Infrastructures en Biologie Sante et AgronomieRegion Ile-de-FrancePlan Cancer, ANR-11-LABX-0039,CHARMMMAT,CHimie des ARchitectures MoléculairesMultifonctionnelles et des MATériaux(2011), and ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017)
Subjects: integumentary system, Physiology, fungi, fungus, strigolactones, Plant Science, perception, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, apocarotenoids, Lactones, Ascomycota, Plant Growth Regulators, α/β-hydrolase, apocarotenoids, Cryphonectria parasitica, D14, fungus, perception, strigolactones, D14, α/β-hydrolase, Heterocyclic Compounds, 3-Ring, Cryphonectria parasitica, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Plant Proteins
Abstract: International audience; Strigolactones (SLs) are plant hormones and important signaling molecules required to promote the arbuscular mycorrhizal (AM) symbiosis. While in plants an α/β-hydrolase, DWARF14 (D14), was shown to act as a receptor that binds and cleaves SLs, the fungal receptor for SLs is unknown.Since AM fungi are currently not genetically tractable, in this study, we used the fungal pathogen Cryphonectria parasitica for which gene deletion protocols exist, as a model, as we have previously shown that it responds to SLs. By means of computational, biochemical and genetic analyses we identified a D14 structural homologue, CpD14.Molecular homology modelling and docking support the prediction that CpD14 interacts with and hydrolyses SLs. The recombinant CpD14 protein shows α/β hydrolytic activity in vitro against the SLs synthetic analogue GR24; its enzymatic activity requires an intact Ser/His/Asp catalytic triad. CpD14 expression in the d14-1 loss-of-function Arabidopsis thaliana line did not rescue the plant mutant phenotype. However, gene inactivation by knock-out homologous recombination reduced fungal sensitivity to SLs.These results indicate that CpD14 is involved in SLs responses in C. parasitica and strengthen the role of SLs as multifunctional molecules acting in plant microbe-interactions.
Published: 2022

49. Chiral oxazolidines acting as transient hydroxyalkyl-functionalized N-heterocyclic carbenes: an efficient route to air stable copper and gold complexes for asymmetric catalysis

Author: Delphine Pichon-Barré, Ziyun Zhang, Aël Cador, Thomas Vives, Thierry Roisnel, Olivier Baslé, Lucie Jarrige, Luigi Cavallo, Laura Falivene, Marc Mauduit, Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), King Abdullah University of Science and Technology (KAUST), Laboratoire de chimie de coordination (LCC), Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Salerno = University of Salerno (UNISA), Agence Nationale de la Recherche [ANR-16-CE07-0019], Rennes Metropole, and ANR-16-CE07-0019,HEL-NHC,Carbènes N-hétérocycliques (NHC) hélicéniques: synthèse, structure, propriétés photophysiques et activité catalytique(2016)
Subjects: [CHIM]Chemical Sciences, General Chemistry
Abstract: International audience; Optically pure oxazolidines were synthesized in nearly quantitative yields from chiral hydroxyalkyl-functionalized imidazolinium salts. Acting as transient chiral diamino N-heterocyclic carbenes (NHCs), these oxazolidines allowed the efficient formation of well-defined copper(i) and gold(i) hydroxyalkyl-NHC complexes, which could be isolated, for the first time, as air stable complexes after silica gel chromatography. Interestingly, X-ray analysis of gold complexes revealed that the hydroxyl-function is not chelated to the metal. Computational studies suggested that both cyclisation to produce oxazolidine and O-H bond elimination to form the transient carbene (prior to coordination) occur through a concerted mechanism. The novel chiral copper-catalysts, as well as oxazolidines alone (copper free), demonstrated excellent performances in asymmetric conjugate addition and allylic alkylation with high regio- and enantio-selectivities (up to 99% ee).
Published: 2022

50. HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions

Author: Ying Huang, Jing An, Sanchari Sircar, Clara Bergis, Chloé Dias Lopes, Xiaoning He, Barbara Da Costa, Feng-Quan Tan, Jeremie Bazin, Javier Antunez-Sanchez, Maria Florencia Mammarella, Ravi-sureshbhai Devani, Rim Brik-Chaouche, Abdelhafid Bendahmane, Florian Frugier, Chongjing Xia, Christophe Rothan, Aline V. Probst, Zouine Mohamed, Catherine Bergounioux, Marianne Delarue, Yijing Zhang, Shaojian Zheng, Martin Crespi, Sotirios Fragkostefanakis, Magdy M. Mahfouz, Federico Ariel, Jose Gutierrez-Marcos, Cécile Raynaud, David Latrasse, Moussa Benhamed, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Warwick [Coventry], Instituto de Agrobiotecnología del Litoral [Santa Fe] (IAL), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Litoral [Santa Fe] (UNL), Southwest University of Science and Technology [Mianyang] (SWUST), Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique, Reproduction et Développement (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), UMR 990, Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM), King Abdullah University of Science and Technology (KAUST), Fudan University [Shanghai], Zhejiang University, Goethe-University Frankfurt am Main, Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), This work was supported by the European Research Council ERC (Project 101044399-3Dwheat), Agence National de la Recherche ANR (ANR-21-CE20-0036-4D Heat Tomato) and by the Institut Universitaire de France (IUF) to M.B. Moreover, this work was supported by China Scholar Council fellowships (201806690005) to Y.H. Figure 6 was created using BioRender (www.biorender.com) with publication permissions., ANR-21-CE20-0036,4D-Heat,Une approche 4D nucleome pour identifier les activateurs contrôlant la réponse au stress thermique de la tomat(2021), and European Project: 101044399,3Dwheat
Subjects: stress thermique, Multidisciplinary, [SDV]Life Sciences [q-bio], General Physics and Astronomy, General Chemistry, Expression des genes, General Biochemistry, Genetics and Molecular Biology, Facteur de transcription, tomate, chaleur, Fruit, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plante, chromatine
Abstract: The complex and dynamic three-dimensional organization of chromatin within the nucleus makes understanding the control of gene expression challenging, but also opens up possible ways to epigenetically modulate gene expression. Because plants are sessile, they evolved sophisticated ways to rapidly modulate gene expression in response to environmental stress, that are thought to be coordinated by changes in chromatin conformation to mediate specific cellular and physiological responses. However, to what extent and how stress induces dynamic changes in chromatin reorganization remains poorly understood. Here, we comprehensively investigated genome-wide chromatin changes associated with transcriptional reprogramming response to heat stress in tomato. Our data show that heat stress induces rapid changes in chromatin architecture, leading to the transient formation of promoter-enhancer contacts, likely driving the expression of heat-stress responsive genes. Furthermore, we demonstrate that chromatin spatial reorganization requires HSFA1a, a transcription factor (TF) essential for heat stress tolerance in tomato. In light of our findings, we propose that TFs play a key role in controlling dynamic transcriptional responses through 3D reconfiguration of promoter-enhancer contacts.
Published: 2023

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