Integrating transposable elements in the 3D genome

Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome

Whole proteome analyses on Ruminiclostridium cellulolyticum show a modulation of the cellulolysis machinery in response to cellulosic materials with subtle differences in chemical and structural properties

Lignocellulosic materials from municipal solid waste emerge as attractive resources for anaerobic digestion biorefinery. To increase the knowledge required for establishing efficient bioprocesses, dynamics of batch fermentation by the cellulolytic bacterium Ruminiclostridium cellulolyticum were compared using three cellulosic materials, paper handkerchief, cotton discs and Whatman filter paper. Fermentation of paper handkerchief occurred the fastest and resulted in a specific metabolic profile: it resulted in the lowest acetate-to-lactate and acetate-to-ethanol ratios. By shotgun proteomic analyses of paper handkerchief and Whatman paper incubations, 151 proteins with significantly different levels were detected, including 20 of the 65 cellulosomal components, 8 non-cellulosomal CAZymes and 44 distinct extracytoplasmic proteins. Consistent with the specific metabolic profile observed, many enzymes from the central carbon catabolic pathways had higher levels in paper handkerchief incubations. Among the quantified CAZymes and cellulosomal components, 10 endoglucanases mainly from the GH9 families and 7 other cellulosomal subunits had lower levels in paper handkerchief incubations. An in-depth characterization of the materials used showed that the lower levels of endoglucanases in paper handkerchief incubations could hypothetically result from its lower crystallinity index (50%) and degree of polymerization (970). By contrast, the higher hemicellulose rate in paper handkerchief (13.87%) did not result in the enhanced expression of enzyme with xylanase as primary activity, including enzymes from the xyl-doc cluster. It suggests the absence, in this material, of molecular structures that specifically lead to xylanase induction. The integrated approach developed in this work shows that subtle differences among cellulosic materials regarding chemical and structural characteristics have significant effects on expressed bacterial functions, in particular the cellulolysis machinery, resulting in different metabolic patterns and degradation dynamics.This work was supported by a grant [R2DS 2010-08] from Conseil Regional d'Ile-de-France through DIM R2DS programs (http://www.r2ds-ile-de-france.com/). Irstea (www.irstea.fr/) contributed to the funding of a PhD grant for the first author. The funders provided support in the form of salaries for author [NB], funding for consumables and laboratory equipment, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Omics Services provided support in the form of salaries for authors [VS, MD], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors [NB, VS, MD] are articulated in the 'author contributions' section.info:eu-repo/semantics/publishedVersio

Graphenes in the absence of metals as carbocatalysts for selective acetylene hydrogenation and alkene hydrogenation

Catalysis makes possible a chemical reaction by increasing the transformation rate. Hydrogenation of carbon-carbon multiple bonds is one of the most important examples of catalytic reactions. Currently, this type of reaction is carried out in petrochemistry at very large scale, using noble metals such as platinum and palladium or first row transition metals such as nickel. Catalysis is dominated by metals and in many cases by precious ones. Here we report that graphene (a single layer of one-atom-thick carbon atoms) can replace metals for hydrogenation of carbon-carbon multiple bonds. Besides alkene hydrogenation, we have shown that graphenes also exhibit high selectivity for the hydrogenation of acetylene in the presence of a large excess of ethylene.This study was financially supported by the Spanish Ministry of Economy and Competitiveness (Severo Ochoa and CTQ2012-32315); and Generalidad Valenciana (Prometeo 21/013) is gratefully acknowledged.Primo Arnau, AM.; Neatu, F.; Florea, M.; Parvulescu, V.; García Gómez, H. (2014). Graphenes in the absence of metals as carbocatalysts for selective acetylene hydrogenation and alkene hydrogenation. Nature Communications. 5:1-9. https://doi.org/10.1038/ncomms6291S195Dreyer, D. R. & Bielawski, C. W. Carbocatalysis: heterogeneous carbons finding utility in synthetic chemistry. Chem. Sci. 2, 1233–1240 (2011).Machado, B. F. & Serp, P. Graphene-based materials for catalysis. Catal. Sci. Technol. 2, 54–75 (2012).Schaetz, A., Zeltner, M. & Stark, W. J. Carbon modifications and surfaces for catalytic organic transformations. ACS Catal. 2, 1267–1284 (2012).Su, D. S. et al. Metal-free heterogeneous catalysis for sustainable chemistry. ChemSusChem 3, 169–180 (2010).Chauhan, S. M. S. & Mishra, S. Use of graphite oxide and graphene oxide as catalysts in the synthesis of dipyrromethane and calix[4]pyrrole. Molecules 16, 7256–7266 (2011).Dreyer, D. R., Jarvis, K. A., Ferreira, P. J. & Bielawski, C. W. Graphite oxide as a carbocatalyst for the preparation of fullerene-reinforced polyester and polyamide nanocomposites. Polym. Chem. 3, 757–766 (2012).Dreyer, D. R., Park, S., Bielawski, C. W. & Ruoff, R. S. The chemistry of graphene oxide. Chem. Soc. Rev. 39, 228–240 (2010).Pyun, J. Graphene oxide as catalyst: application of carbon materials beyond nanotechnology. Angew. Chem. Int. Ed. 50, 46–48 (2011).Rourke, J. P. et al. The real graphene oxide revealed: stripping the oxidative debris from the graphene-like sheets. Angew. Chem. Int. Ed. 50, 3173–3177 (2011).Sun, H. et al. Reduced graphene oxide for catalytic oxidation of aqueous organic pollutants. ACS Appl. Mater. Interf. 4, 5466–5471 (2012).Dreyer, D. R., Jia, H. P. & Bielawski, C. W. Graphene oxide: a convenient carbocatalyst for facilitating oxidation and hydration reactions. Angew. Chem. Int. Ed. 49, 6813–6816 (2010).Dreyer, D. R., Jia, H. P., Todd, A. D., Geng, J. X. & Bielawski, C. W. Graphite oxide: a selective and highly efficient oxidant of thiols and sulfides. Org. Biomol. Chem. 9, 7292–7295 (2011).Hayashi, M. Oxidation using activated carbon and molecular oxygen system. Chem. Rec. 8, 252–267 (2008).Jia, H. P., Dreyer, D. R. & Bielawski, C. W. C-H oxidation using graphite oxide. Tetrahedron 67, 4431–4434 (2011).Kumar, A. V. & Rao, K. R. Recyclable graphite oxide catalyzed Friedel-Crafts addition of indoles to alpha, beta-unsaturated ketones. Tetrahedron Lett. 52, 5188–5191 (2011).Soria-Sanchez, M. et al. Carbon nanostructure materials as direct catalysts for phenol oxidation in aqueous phase. Appl. Catal. B Environ. 104, 101–109 (2011).Verma, S. et al. Graphene oxide: an efficient and reusable carbocatalyst for aza-Michael addition of amines to activated alkenes. Chem. Commun. 47, 12673–12675 (2011).Yu, H. et al. Solvent-free catalytic dehydrative etherification of benzyl alcohol over graphene oxide. Chem. Phys. Lett. 583, 146–150 (2013).Holschumacher, D., Bannenberg, T., Hrib, C. G., Jones, P. G. & Tamm, M. Heterolytic dihydrogen activation by a frustrated carbene-borane Lewis pair. Angew. Chem. Int. Ed. 47, 7428–7432 (2008).Staubitz, A., Robertson, A. P. M., Sloan, M. E. & Manners, I. Amine- and phosphine-borane adducts: new interest in old molecules. Chem. Rev. 110, 4023–4078 (2010).Stephan, D. W. & Erker, G. Frustrated Lewis Pairs: Metal-free Hydrogen Activation and More. Angew. Chem. Int. Ed. 49, 46–76 (2010).Poh, H. L., Sanek, F., Sofer, Z. & Pumera, M. High-pressure hydrogenation of graphene: towards graphane. Nanoscale 4, 7006–7011 (2012).Sofo, J. O., Chaudhari, A. S. & Barber, G. D. Graphane: A two-dimensional hydrocarbon. J. Phys. Chem. B 75, 153401 (2007).Elias, D. C. et al. Control of graphene’s properties by reversible hydrogenation: evidence for graphane. Science 323, 610–613 (2009).Despiau-Pujo, E. et al. Elementary processes of H2 plasma-graphene interaction: a combined molecular dynamics and density functional theory study. J. Appl. Phys. 113, 114302 (2013).Xu, L. & Ge, Q. Effects of defects and dopants in graphene on hydrogen interaction in graphene-supported NaAlH4. Int. J. Hydrogen Energy 38, 3670–3680 (2013).Perhun, T. I., Bychko, I. B., Trypolsky, A. I. & Strizhak, P. E. Catalytic properties of graphene material in the hydrogenation of ethylene. Theor. Exp. Chem. 48, 367–370 (2013).Hummers, W. S. & Offeman, R. E. Preparation of graphitic oxide. J. Am. Chem. Soc. 80, 1339 (1958).Dhakshinamoorthy, A., Primo, A., Concepcion, P., Alvaro, M. & Garcia, H. Doped graphene as a metal-free carbocatalyst for the selective aerobic oxidation of benzylic hydrocarbons, cyclooctane and styrene. Chem. Eur. J. 19, 7547–7554 (2013).Latorre-Sanchez, M., Primo, A. & Garcia, H. P-doped graphene obtained by pyrolysis of modified alginate as a photocatalyst for hydrogen generation from water-methanol mixtures. Angew. Chem. Int. Ed. 52, 11813–11816 (2013).Primo, A., Sanchez, E., Delgado, J. M. & Garcia, H. High-yield production of N-doped graphitic platelets by aqueous exfoliation of pyrolyzed chitosan. Carbon N. Y. 68, 777–783 (2014).Stankovich, S. et al. Synthesis of graphene-based nanosheets via chemical reduction of exfoliated graphite oxide. Carbon N. Y. 45, 1558–1565 (2007).Pumera, M. & Wong, C. H. A. Graphane and hydrogenated graphene. Chem. Soc. Rev. 42, 5987–5995 (2013).Teschner, D. et al. The roles of subsurface carbon and hydrogen in palladium-catalyzed alkyne hydrogenation. Science 320, 86–89 (2008).Bridier, B., Lopez, N. & Perez-Ramirez, J. Molecular understanding of alkyne hydrogenation for the design of selective catalysts. Dalton Trans. 39, 8412–8419 (2010).Flick, K., Herion, C. & Allmann, H. Palladium-haltiger Trägerkatalysator zur selektiven katalytischen Hydrierung von Acetylen in Kohlenwasserstoffströmen. EP764463-A; EP764463-A2; DE19535402-A1; JP9141097-A; CA2185721-A; KR97014834-A; MX9604031-A1; US5847250-A; US5856262-A; TW388722-A; MX195137-B; CN1151908-A; EP764463-B1; DE59610365-G; ES2197222-T3; KR418161-B; CN1081487-C; JP3939787-B2; CA2185721-C (1997).Gartside, R. J. et al. Improved olefin plant recovery system employing a combination of catalytic distillation and fixed bed catalytic steps. 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Proc. Natl Acad. Sci. USA 109, 12899–12904 (2012).Vile, G., Almora-Barrios, N., Mitchell, S., Lopez, N. & Perez-Ramirez, J. From the lindlar catalyst to supported ligand-modified palladium nanoparticles: selectivity patterns and accessibility constraints in the continuous-flow three-phase hydrogenation of acetylenic compounds. Chemistry 20, 5849–5849 (2014).Gurrath, M. et al. Palladium catalysts on activated carbon supports—Influence of reduction temperature, origin of the support and pretreatments of the carbon surface. Carbon N. Y. 38, 1241–1255 (2000).Stephan, D. W. ‘Frustrated Lewis pairs’: a concept for new reactivity and catalysis. Org. Biomol. Chem. 6, 1535–1539 (2008).Stephan, D. W. Frustrated Lewis pairs: a new strategy to small molecule activation and hydrogenation catalysis. Dalton Trans. 17, 3129–3136 (2009).Chase, P. A., Jurca, T. & Stephan, D. W. Lewis acid-catalyzed hydrogenation: B(C6F5)3-mediated reduction of imines and nitriles with H2. Chem. 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Genome-Wide Distribution of RNA-DNA Hybrids Identifies RNase H Targets in tRNA Genes, Retrotransposons and Mitochondria

During transcription, the nascent RNA can invade the DNA template, forming extended RNA-DNA duplexes (R-loops). Here we employ ChIP-seq in strains expressing or lacking RNase H to map targets of RNase H activity throughout the budding yeast genome. In wild-type strains, R-loops were readily detected over the 35S rDNA region, transcribed by Pol I, and over the 5S rDNA, transcribed by Pol III. In strains lacking RNase H activity, R-loops were elevated over other Pol III genes, notably tRNAs, SCR1 and U6 snRNA, and were also associated with the cDNAs of endogenous TY1 retrotransposons, which showed increased rates of mobility to the 5'-flanking regions of tRNA genes. Unexpectedly, R-loops were also associated with mitochondrial genes in the absence of RNase H1, but not of RNase H2. Finally, R-loops were detected on actively transcribed protein-coding genes in the wild-type, particularly over the second exon of spliced ribosomal protein genes

La qualification territoriale des produits dans les processus d’activation des SYAL. Le cas des fromageries rurales en Amérique Latine

En Amérique Latine, depuis la fin des années 1990, une nouvelle voie de développement de l’agro-industrie rurale (AIR) a été ouverte avec les Systèmes Agroalimentaires Localisés (SYAL). Elle est apparue à partir des relations qui existent entre des concentrations géographiques d’AIR et le territoire, pour faire face aux nouveaux défis posés par la mondialisation : recomposition des circuits de commercialisation, concurrence accrue avec les produits nationaux et importés, nouvelles exigences des consommateurs, notamment en termes de qualité. Cette dynamique est particulièrement notoire dans le secteur du lait et de la fromagerie rurale, où l’on constate l’existence de concentrations géographiques d’AIR que l’on peut assimiler à des SYAL du fait de leur capacité à s’organiser dans le but de mettre en valeur des ressources territoriales communes. L’analyse de cette faculté collective a conduit à la définition du concept « d’activation des SYAL ». L’objectif de cette communication est d’illustrer le concept d’activation des SYAL à travers l’analyse de trois cas de concentrations d’agro-industries fromagères en Amérique Latine qui connaissent des dynamiques collectives liées à la qualification territoriale des produits. Il apparaît en effet que ces dynamiques sont une composante de plus en plus marquée dans la constitution des SYAL fromagers en Amérique Latine. Il s’agit en particulier de discuter les conditions « internes » favorables à la qualification et les conditions « externes » permettant sa reconnaissance (signe de qualité). Nous montrons également qu’au-delà de son intérêt économique, la qualification territoriale des fromages artisanaux vise la reconnaissance de la typicité face aux menaces représentées par les usurpations d’appellation et la tendance à la normalisation des produits alimentaires. Finalement, nous mettons en évidence les conditions nécessaires à la qualification territoriale vue comme un outil pour l’activation de ressources spécifiques (relations de proximité et de confiance, environnement favorable, action collective, diffusion de l’innovation et des savoir-faire). Nous insistons en particulier sur le nécessaire apprentissage collectif induit par les démarches de qualification territoriale. Selon le cas en effet, la qualification s’accompagne pour les producteurs d’une réappropriation du patrimoine collectif, d’un apprentissage de l’action collective et de la négociation, ou d’une appropriation de nouvelles techniques et d’un savoir faire. L’apprentissage collectif concerne également les structures d’appui aux producteurs à travers la construction de relations de partenariat, mais aussi les instances administratives en charge de la gestion des demandes d’obtention des signes de qualité, pour qui ces démarches sont nouvelles et demandent donc un apprentissage institutionnel

Predicting fretting-fatigue endurance of rotating bending shrink-fitted assemblies using a sequential RUIZ-SWT approach: The effect of entrapped debris layer

International audienceFretting-fatigue damage often appears in shaft shrink-fitted assemblies submitted to rotating bending. This paperfocuses on the influence of the sleeve edge geometry on such damage. Rotating bending tests have been performed and broken and unbroken specimens have been expertized confirming fretting-fatigue phenomena. A 3D finite element method model was developed to evaluate the sliding and opening lengths. A sequential tribological - fatigue stress analysis strategy allowed the prediction of the maximum crack location ( Ruiz criterion)then the estimation of the fatigue endurance of the assembly using the SWT criterion. The last step of thisσSWT(XΓmax) approach considers the presence of a debris layer within the contact to improve the consistency ofthe service life prediction

Ceria in hydrogenation catalysis: High selectivity in the conversion of alkynes to olefins

Active and selective: Ceria shows a high activity and selectivity in the gas-phase hydrogenation of alkynes to olefins (see picture). This unprecedented behavior has direct impact on the purification of olefin streams and, more importantly, it opens new perspectives for exploring this fascinating oxide as a catalyst for the selective hydrogenation of other functional groups

Contribution of Confocal Laser Scanning Microscopy in Deciphering Biofilm Tridimensional Structure and Reactivity

International audienceConfocal laser scanning microscopy (CLSM) became in last years an invaluable technique to study biofilms since it enables researchers to explore noninvasively the dynamic architecture and the reactivity of these biological edifices. The constant development of fluorescent markers and genetic tools along with the improvement of spatial, spectral, and temporal resolution of imaging facilities offers new opportunities to better decipher microbial biofilm properties. In this contribution, we proposed to describe the contribution of CLSM to the study of biofilm architecture and reactivity throughout two different illustrative approaches

Surface state during activation and reaction of high performing multi metallic alkyne hydrogenation catalysts

In partial hydrogenation of highly unsaturated compounds, high-performance heterogeneous catalysts usually consist of multi-metallic systems providing enhanced selectivity. These materials often undergo complex segregation phenomena and to understand their function, a surface-sensitive in situ methodology is crucial. Recently, we reported a novel family of ternary Cu–Ni–Fe catalysts for propyne hydrogenation with exceptional selectivity to propene. Herein, we detail our study on the surface composition and electronic state of two representative samples (Cu2.75Ni0.25Fe and Cu3Fe) using in situ X-ray photoelectron (XPS) and X-ray absorption (XAS) spectroscopies. Surface segregation phenomena during activation of the catalyst precursors (calcination and reduction) and hydrogenation reaction were evaluated. The multiple functions of nickel in the catalyst, which account for the extraordinary alkene selectivity, are unravelled